Pierrick Roger
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 6eb1625 |
| git_last_commit_date: 2023-10-24 11:36:37 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:38:55 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 198/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.9.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.9.0.tar.gz |
| StartedAt: 2024-03-02 00:47:04 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 00:51:29 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 265.5 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 4.654 1.461 40.609
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-03-02 00:49:17.930][biodb::testContext]
biodb.INFO [2024-03-02 00:49:17.942][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:49:17.945][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-02 00:49:17.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:49:17.953][biodb::testContext]
biodb.INFO [2024-03-02 00:49:17.971][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:49:17.977][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:49:17.997][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:49:18.000][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:49:18.003][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.017][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:49:18.091][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.104][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:49:18.107][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.123][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:49:18.126][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:49:18.129][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:49:18.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.144][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:49:18.148][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:49:18.151][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.167][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:49:18.170][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:49:18.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.184][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:49:18.188][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:49:18.192][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:49:18.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.204][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:49:18.207][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.220][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:49:18.224][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:49:18.226][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:49:18.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.241][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:49:18.246][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:49:18.250][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:49:18.274][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:49:18.276][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:49:18.279][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:49:18.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.290][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:49:18.294][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:49:18.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.303][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:49:18.307][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:49:18.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.317][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:49:18.320][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:49:18.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.330][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:49:18.333][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:49:18.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.341][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[2024-03-02 00:49:18.344][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:49:18.346][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:49:18.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.355][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:49:18.358][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:49:18.380][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:49:18.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.389][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:49:18.392][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:49:18.394][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:49:18.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.409][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:49:18.504][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.552][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:49:18.556][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:49:18.561][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.570][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.573][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:49:18.575][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:49:18.579][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.582][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:49:18.584][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:49:18.586][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.590][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.592][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:49:18.592][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:49:18.592][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:49:18.592][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:49:18.592][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:49:18.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:49:18.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:49:18.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.613][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.616][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:49:18.618][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:49:18.621][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.625][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.628][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:49:18.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:49:18.640][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:49:18.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.650][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.656][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:49:18.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:49:18.661][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.664][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:49:18.666][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:49:18.669][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.672][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.674][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:49:18.674][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:49:18.674][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:49:18.674][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:49:18.674][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:49:18.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:49:18.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:49:18.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.695][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.697][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.699][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:49:18.702][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:49:18.706][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.710][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.713][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:49:18.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.721][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:49:18.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:49:18.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.734][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.736][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.741][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:49:18.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:49:18.746][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.750][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:49:18.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:49:18.756][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.759][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.761][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:49:18.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.771][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:49:18.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.781][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.783][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:49:18.789][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:49:18.791][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.793][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.795][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:49:18.800][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.803][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:49:18.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.808][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:49:18.811][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.816][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.821][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:49:18.824][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:49:18.827][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.829][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:49:18.831][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:49:18.834][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.837][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:18.840][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:49:18.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.849][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:49:18.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:18.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:18.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:49:18.864][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.866][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:49:18.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:49:18.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:18.876][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:49:18.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:49:18.897][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.924][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[2024-03-02 00:49:18.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:18.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.986][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[2024-03-02 00:49:18.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:18.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:18.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:18.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:18.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.009][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[2024-03-02 00:49:19.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.060][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[2024-03-02 00:49:19.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.084][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[2024-03-02 00:49:19.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.098][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:49:19.107][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:49:19.111][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:49:19.116][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:49:19.120][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:49:19.123][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:49:19.127][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:49:19.130][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:49:19.134][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:49:19.137][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:49:19.140][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:49:19.143][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:49:19.147][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:49:19.150][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:49:19.153][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:49:19.157][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:49:19.161][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:49:19.164][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:49:19.167][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:49:19.171][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:49:19.174][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:49:19.178][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:49:19.183][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:49:19.186][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:49:19.190][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:49:19.193][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:49:19.197][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:49:19.201][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:49:19.205][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:49:19.208][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:49:19.212][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:49:19.216][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:49:19.219][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:49:19.223][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:49:19.228][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:49:19.231][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:49:19.234][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:49:19.238][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:49:19.242][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:49:19.245][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:49:19.250][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:49:19.253][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:49:19.257][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:49:19.262][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:49:19.265][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:49:19.270][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:49:19.274][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:49:19.279][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:49:19.283][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:49:19.286][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:49:19.289][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:49:19.294][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:49:19.298][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:49:19.302][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:49:19.305][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:49:19.309][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:49:19.313][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:49:19.318][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:49:19.322][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:49:19.326][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:49:19.330][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:49:19.334][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:49:19.337][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:49:19.342][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:49:19.346][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:49:19.350][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:49:19.354][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:49:19.357][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:49:19.362][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:49:19.366][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:49:19.369][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:49:19.373][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:49:19.378][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:49:19.383][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:49:19.387][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:49:19.391][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:49:19.394][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:49:19.398][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:49:19.402][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:49:19.405][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:49:19.409][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:49:19.412][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:49:19.416][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:49:19.435][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:49:19.439][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:49:19.459][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:49:19.461][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.465][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.529][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[2024-03-02 00:49:19.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.751][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[2024-03-02 00:49:19.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:49:19.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:19.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:19.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:19.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:19.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:19.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:19.779][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-02 00:49:19.805][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-02 00:49:19.809][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:19.813][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:49:19.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:19.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:49:19.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:19.822][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:49:19.827][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:19.829][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-02 00:49:19.832][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-02 00:49:19.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:49:19.837][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:19.839][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-02 00:49:19.842][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-02 00:49:19.845][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-02 00:49:19.852][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:49:19.854][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:49:19.854][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:49:19.854][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:49:19.856][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 00:49:19.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:19.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:19.867][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:49:19.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:49:19.871][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:49:19.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:49:19.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:19.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-02 00:49:19.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:49:19.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:49:19.883][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:49:19.887][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-02 00:49:19.887][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-02 00:49:19.902][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:49:19.905][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:49:19.910][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-02 00:49:19.913][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:49:19.917][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:49:19.923][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:49:19.976][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-02 00:49:19.979][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-02 00:49:19.991][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-02 00:49:20.000][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-02 00:49:20.009][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:49:20.011][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:49:20.014][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-02 00:49:20.017][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-02 00:49:20.050][biodb::testThat]
biodb.INFO [2024-03-02 00:49:20.053][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-02 00:49:20.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:20.058][biodb::testThat]
biodb.TRACE[2024-03-02 00:49:20.068][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-03-02 00:49:20.072][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:20.079][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:20.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:20.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:20.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:20.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:20.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:20.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:20.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:20.162][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.164][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.169][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.217][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:20.219][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:20.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.226][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:20.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:20.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.313][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:20.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:20.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.320][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:20.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:20.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.331][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:20.334][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:20.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.340][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:20.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:20.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.355][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.358][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.365][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.378][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:20.380][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:20.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.385][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:20.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:20.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.399][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:20.402][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.408][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:20.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.421][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:20.424][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:20.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.428][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:20.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:20.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.442][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:20.444][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:20.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.449][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:20.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.461][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:20.464][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:20.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.469][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.483][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:20.486][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:20.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.491][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:20.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:20.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:20.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:20.731][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-03-02 00:49:20.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:20.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:20.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:20.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:20.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:20.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:20.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:20.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:20.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.909][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:20.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:20.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:20.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:20.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:20.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:20.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.244][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.246][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.252][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:21.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:21.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.344][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:21.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:21.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:21.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:21.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:21.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:21.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.410][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:21.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:21.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.417][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:21.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:21.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:21.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:21.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:21.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:21.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.478][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:21.481][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:21.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.487][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:21.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:21.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.545][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.548][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.552][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:21.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.619][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.621][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.626][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:21.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.655][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:21.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:21.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.664][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:21.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.675][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:21.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:21.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.684][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:21.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:21.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.690][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.693][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:21.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.728][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.748][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.750][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.755][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.757][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:21.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.817][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.819][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.824][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.827][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:21.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.859][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:21.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:21.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:21.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:21.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.881][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:21.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:21.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.892][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:21.895][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:21.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.900][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.902][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:21.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:21.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.977][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:21.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:21.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:21.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.059][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.090][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.093][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.097][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.109][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:22.113][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:22.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.118][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.132][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:22.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:22.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.141][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.151][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.154][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.159][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.172][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.177][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.185][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.198][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.201][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.205][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.218][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:22.221][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:22.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.226][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.237][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.240][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.245][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.258][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-02 00:49:22.261][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:22.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.265][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.275][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.278][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.282][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.297][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:22.300][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:22.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.304][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:49:22.328][biodb::testThat]
biodb.INFO [2024-03-02 00:49:22.331][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-02 00:49:22.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:22.335][biodb::testThat]
biodb.DEBUG[2024-03-02 00:49:22.370][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-03-02 00:49:22.384][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:22.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-03-02 00:49:22.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:22.398][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-03-02 00:49:22.401][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:22.464][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:22.466][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:22.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:22.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:22.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:22.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:22.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:22.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:22.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:22.505][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.509][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.513][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.565][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:22.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:22.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.572][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.575][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:22.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:22.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.584][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:22.587][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:22.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.591][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.594][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:22.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.603][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.605][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.609][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:22.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:22.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.620][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.622][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.627][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:22.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.638][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.640][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.645][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.647][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:22.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.656][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:22.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:22.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.664][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:22.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:22.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.677][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.680][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.685][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:22.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.696][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.698][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.703][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.715][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:22.717][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:22.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.721][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.724][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:22.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:22.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.733][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:22.735][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:22.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.739][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.742][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:22.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:22.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:22.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:22.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:22.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:22.843][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-03-02 00:49:22.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 00:49:22.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 00:49:22.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 00:49:22.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 00:49:22.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 00:49:22.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 00:49:22.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:49:22.893][biodb::testThat]
biodb.INFO [2024-03-02 00:49:22.895][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-02 00:49:22.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:22.899][biodb::testThat]
biodb.TRACE[2024-03-02 00:49:22.905][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.907][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.911][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:22.914][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-03-02 00:49:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:22.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:22.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:22.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:23.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:23.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:23.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:23.016][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-03-02 00:49:23.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-02 00:49:23.080][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:49:23.119][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-02 00:49:23.122][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:23.125][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-02 00:49:23.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:23.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:23.198][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:23.202][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-02 00:49:24.003][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-02 00:49:24.527][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:24.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-03-02 00:49:24.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-03-02 00:49:24.582][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-03-02 00:49:24.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:24.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:24.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:24.617][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:24.620][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:24.622][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:24.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:24.626][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:49:24.635][biodb::testThat]
biodb.INFO [2024-03-02 00:49:24.638][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-02 00:49:24.640][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:24.642][biodb::testThat]
biodb.TRACE[2024-03-02 00:49:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:24.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:24.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:24.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:24.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:24.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:24.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:24.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:24.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:24.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:24.887][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:24.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:49:24.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:49:24.906][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:24.911][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-03-02 00:49:24.958][biodb::testThat]
biodb.INFO [2024-03-02 00:49:24.960][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-02 00:49:24.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:24.965][biodb::testThat]
biodb.TRACE[2024-03-02 00:49:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:25.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.097][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.112][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:25.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:25.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.124][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:25.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:25.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:25.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:25.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.269][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.280][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 00:49:25.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.292][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:25.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 00:49:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:25.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:25.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 00:49:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:49:25.328][biodb::testThat]
biodb.INFO [2024-03-02 00:49:25.331][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-02 00:49:25.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:25.336][biodb::testThat]
biodb.INFO [2024-03-02 00:49:25.355][biodb::testThat]
biodb.INFO [2024-03-02 00:49:25.357][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-02 00:49:25.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:25.363][biodb::testThat]
biodb.INFO [2024-03-02 00:49:25.389][biodb::testThat]
biodb.INFO [2024-03-02 00:49:25.391][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-02 00:49:25.393][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:25.395][biodb::testThat]
biodb.DEBUG[2024-03-02 00:49:25.405][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-03-02 00:49:25.957][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-03-02 00:49:26.790][biodb::testThat]
biodb.INFO [2024-03-02 00:49:26.793][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-02 00:49:26.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:26.798][biodb::testThat]
biodb.DEBUG[2024-03-02 00:49:27.215][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-03-02 00:49:27.654][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:27.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:27.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:27.660][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:27.662][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:27.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:27.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:27.668][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:49:27.671][biodb::testThat]
biodb.INFO [2024-03-02 00:49:27.673][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-02 00:49:27.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:49:27.677][biodb::testThat]
biodb.TRACE[2024-03-02 00:49:27.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:27.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:27.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:27.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:27.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:27.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:27.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:27.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:27.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:27.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:27.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:27.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:27.902][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:27.911][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:49:27.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:49:27.921][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:27.924][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-02 00:49:28.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:28.100][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:49:28.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:49:28.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:28.109][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-03-02 00:49:28.140][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:49:28.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:49:28.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:28.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:28.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:28.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:28.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:28.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:28.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:28.219][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:28.276][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:28.278][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:28.338][private$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[2024-03-02 00:49:28.725][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[2024-03-02 00:49:29.110][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:29.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-03-02 00:49:29.123][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-03-02 00:49:29.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:29.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:29.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:29.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:29.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:29.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:29.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:29.152][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-03-02 00:49:29.267][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:29.271][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-03-02 00:49:29.274][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:29.277][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:29.280][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:29.282][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:29.285][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:29.287][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:29.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:29.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:29.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:29.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:29.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:29.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:29.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:29.317][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-03-02 00:49:29.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:29.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:29.329][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-03-02 00:49:29.719][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-03-02 00:49:30.103][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:30.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-03-02 00:49:30.157][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-03-02 00:49:30.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-03-02 00:49:30.168][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:30.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:30.175][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:30.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:30.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:30.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:30.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:30.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:30.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:30.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:30.205][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.212][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.224][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:30.227][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:30.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.231][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:30.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:30.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.243][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:30.246][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:30.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.250][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:30.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:30.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.263][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:30.265][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:30.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.270][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:30.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.282][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:30.285][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:30.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.290][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:30.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:30.305][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:30.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.310][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.313][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:30.316][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.320][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:30.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:30.335][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:30.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.339][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:30.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:30.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:30.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.358][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:30.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:30.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:30.374][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:30.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.378][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:30.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:30.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.390][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:30.393][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:30.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.397][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:30.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:30.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:30.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:30.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:30.632][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-03-02 00:49:30.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:30.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:30.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:30.691][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:30.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:30.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:30.706][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-02 00:49:31.090][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-02 00:49:31.471][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:31.476][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-03-02 00:49:31.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-03-02 00:49:31.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:31.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:31.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:31.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:31.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:31.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:31.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:31.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:31.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:31.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:31.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:31.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:31.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:31.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:31.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:31.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:31.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:31.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:31.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:31.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:31.627][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-03-02 00:49:31.629][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:31.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-03-02 00:49:31.635][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:31.638][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:31.640][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:31.643][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:31.645][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:31.647][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:31.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:31.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:31.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:31.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:31.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:31.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:31.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:31.716][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-03-02 00:49:31.722][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:31.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:31.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-03-02 00:49:32.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-03-02 00:49:32.486][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:32.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-03-02 00:49:32.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-03-02 00:49:32.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-03-02 00:49:33.084][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:33.087][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:33.089][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:33.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:33.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:33.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:33.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:33.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:33.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:33.116][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[2024-03-02 00:49:33.120][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.127][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.141][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:33.143][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:33.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.151][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.154][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:33.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:33.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.164][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:33.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:33.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.172][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:33.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:33.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:33.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.190][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:33.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:33.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:33.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:33.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.213][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.224][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:33.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:33.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.231][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.233][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:33.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.241][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.244][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:33.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.254][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:33.256][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:33.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.261][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:33.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:33.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.273][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:33.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:33.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.278][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:33.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:33.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.290][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:33.293][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:33.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.297][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:33.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:33.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.320][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:33.323][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:33.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.326][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:33.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:33.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:33.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:33.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:33.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:33.436][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-03-02 00:49:33.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:33.516][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:49:33.527][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:49:33.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:49:33.537][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:49:33.541][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-02 00:49:33.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:33.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:33.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:33.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:33.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:33.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:33.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:33.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:33.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:33.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:33.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:33.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:33.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:33.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:33.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:33.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:33.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:33.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:33.645][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-03-02 00:49:33.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:33.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-03-02 00:49:33.654][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:33.664][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:33.668][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:33.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:33.672][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:33.674][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:33.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:33.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:33.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:33.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:33.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:33.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:33.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:33.708][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-03-02 00:49:33.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:33.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:33.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-03-02 00:49:34.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-03-02 00:49:34.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:34.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-03-02 00:49:34.506][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-03-02 00:49:34.512][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-03-02 00:49:34.516][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:34.519][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:34.522][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:34.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:34.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:34.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:34.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:34.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:34.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:34.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:34.553][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.560][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.573][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:34.576][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:34.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.581][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.583][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:34.586][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:34.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.590][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:34.597][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:34.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.601][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:34.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:34.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.611][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.614][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:34.617][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:34.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.621][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.624][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:34.627][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.631][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.633][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:34.636][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:34.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.640][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.643][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:34.646][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:34.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.650][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:34.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.662][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:34.664][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:34.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.668][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.671][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:34.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.681][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:34.683][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:34.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.688][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:34.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:34.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:34.796][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-03-02 00:49:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:34.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:34.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:34.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:34.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:34.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:34.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:34.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:34.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:34.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:34.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:34.863][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-03-02 00:49:34.866][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:34.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-03-02 00:49:34.872][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:34.874][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:34.877][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:34.879][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:34.881][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:34.883][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:34.889][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:34.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:34.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:34.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:34.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:34.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:34.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:34.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-03-02 00:49:34.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:34.921][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:34.924][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-03-02 00:49:35.310][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-03-02 00:49:35.689][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:35.694][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-03-02 00:49:35.703][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-03-02 00:49:35.709][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-03-02 00:49:35.712][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:35.715][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:35.718][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:35.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:35.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:35.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:35.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:35.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:35.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:35.742][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[2024-03-02 00:49:35.747][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.754][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.766][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:35.769][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:35.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.773][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.776][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:35.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:35.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.783][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.786][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:35.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:35.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.794][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.797][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:35.809][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:35.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.819][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.822][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:35.826][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:35.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.830][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.833][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:35.837][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:35.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.841][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.844][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:35.847][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:35.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.851][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.854][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:35.857][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:35.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.862][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:35.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:35.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.879][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:35.882][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:35.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.886][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.889][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:35.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:35.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.901][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:35.907][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:35.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.912][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:35.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:35.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:35.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:35.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:36.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:36.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:36.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:36.032][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-03-02 00:49:36.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:36.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:36.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:36.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:36.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:36.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:36.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:36.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:36.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:36.125][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-03-02 00:49:36.128][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:36.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-03-02 00:49:36.135][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:36.138][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:36.140][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:36.142][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:36.145][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:36.148][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:36.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:36.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:36.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:36.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:36.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:36.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:36.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:36.192][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-03-02 00:49:36.199][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:36.202][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:36.206][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-03-02 00:49:36.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-03-02 00:49:36.973][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:36.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-03-02 00:49:36.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-03-02 00:49:36.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-03-02 00:49:36.994][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:36.997][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:37.000][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:37.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:37.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:37.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:37.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:37.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:37.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:37.023][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[2024-03-02 00:49:37.028][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.031][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.035][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.047][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:37.049][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:37.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.054][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.056][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:37.059][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:37.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.063][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.066][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:37.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:37.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.073][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.076][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:37.078][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:37.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.083][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:37.088][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:37.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:37.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.102][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:37.107][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:37.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.111][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.113][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:37.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:37.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.120][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:37.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.133][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:37.136][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:37.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.140][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:37.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:37.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.152][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:37.154][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:37.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.159][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:37.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:37.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:37.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:37.277][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-03-02 00:49:37.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:37.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:37.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:37.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:37.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:37.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:37.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:37.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:37.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:37.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:37.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:37.366][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-03-02 00:49:37.368][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:37.372][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-03-02 00:49:37.375][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:37.377][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:37.382][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:37.384][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:37.387][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:37.389][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:37.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:37.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:37.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:37.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:37.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:37.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:37.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:37.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-03-02 00:49:37.437][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:37.440][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:37.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-03-02 00:49:37.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-03-02 00:49:38.219][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:38.223][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-03-02 00:49:38.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-03-02 00:49:38.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-03-02 00:49:38.241][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:38.244][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:38.247][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:38.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:38.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:38.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:38.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:38.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:38.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:38.272][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[2024-03-02 00:49:38.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.285][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.298][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:38.300][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:38.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.305][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.308][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:38.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:38.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.317][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:38.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:38.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.324][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:38.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:38.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:38.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:38.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.344][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:38.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.364][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:38.372][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:38.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.376][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:38.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:38.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.393][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:38.396][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:38.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.400][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.407][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:38.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:38.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.416][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:38.419][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.423][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.435][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:38.438][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:38.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.442][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:38.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:38.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.458][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:38.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:38.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.466][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:38.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:38.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.483][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:38.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:38.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.490][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.493][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:38.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:38.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.504][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:38.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:38.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.511][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:38.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:38.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:38.641][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-03-02 00:49:38.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:38.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:38.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:38.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:38.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:38.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:38.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:38.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:38.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:38.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:38.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:38.705][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-03-02 00:49:38.707][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:38.711][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-03-02 00:49:38.749][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:38.754][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:38.758][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:38.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:38.763][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:38.765][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:38.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:38.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:38.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:38.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:38.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:38.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:38.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:38.805][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-03-02 00:49:38.811][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:38.815][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:38.819][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-03-02 00:49:39.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-03-02 00:49:39.598][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:39.602][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-03-02 00:49:39.942][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-03-02 00:49:40.065][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-03-02 00:49:40.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:40.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:40.157][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:40.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:40.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:40.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:40.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:40.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:40.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:40.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:40.186][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.189][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.193][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.206][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:40.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:40.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.213][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.216][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.226][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:40.228][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:40.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.233][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:40.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:40.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.246][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:40.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:40.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.253][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:40.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.329][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:40.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:40.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.336][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:40.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:40.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.359][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:40.362][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:40.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.366][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.369][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:40.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.378][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:40.381][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.385][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.388][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:40.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.400][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:40.425][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:40.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.429][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:40.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:40.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:40.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:40.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.466][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:40.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:40.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.478][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:40.491][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:40.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.496][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.499][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:40.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:40.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.523][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:40.526][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:40.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.530][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:40.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:40.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:40.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:40.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:40.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:40.629][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-03-02 00:49:40.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:40.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:40.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:40.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:40.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:40.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:40.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:40.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:40.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:40.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:40.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:40.681][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-03-02 00:49:40.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:40.687][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-03-02 00:49:40.690][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:40.692][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:40.694][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:40.697][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:40.699][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:40.701][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:40.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:40.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:40.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:40.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:40.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:40.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:40.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:40.732][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-03-02 00:49:40.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:40.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:40.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-03-02 00:49:41.126][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-03-02 00:49:41.505][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:41.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-03-02 00:49:41.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-03-02 00:49:41.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-03-02 00:49:41.737][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:41.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:41.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:41.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:41.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:41.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:41.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:41.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:41.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:41.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:41.786][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:41.790][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:41.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.796][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:41.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.809][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:41.812][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:41.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.858][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.861][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:41.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:41.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.874][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:41.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:41.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.882][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:41.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:41.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.900][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:41.906][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:41.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.911][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.927][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:41.930][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:41.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.934][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:41.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:41.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:41.951][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:41.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.956][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.961][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:41.963][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:41.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.968][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.972][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:41.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:41.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:41.985][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:41.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:41.990][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:41.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:41.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:41.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.003][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:42.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:42.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.010][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:42.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:42.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.022][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:42.024][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:42.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.028][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.035][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:42.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:42.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:42.048][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:42.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.053][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.056][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:42.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:42.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:42.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:42.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:42.165][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-03-02 00:49:42.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:42.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:42.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:42.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:42.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:42.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:42.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:42.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:42.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:42.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:42.232][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-03-02 00:49:42.235][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:42.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-03-02 00:49:42.243][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:42.245][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:42.248][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:42.252][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:42.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:42.259][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:42.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:42.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:42.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:42.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:42.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:42.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:42.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:42.291][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-03-02 00:49:42.298][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:42.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:42.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-03-02 00:49:42.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-03-02 00:49:43.064][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:43.068][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-03-02 00:49:43.611][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-03-02 00:49:44.021][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-03-02 00:49:44.463][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:44.477][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:44.480][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:44.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:44.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:44.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:44.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:44.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:44.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:44.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:44.512][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.519][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.532][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:44.535][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:44.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.540][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:44.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:44.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.556][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:44.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:44.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.568][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:44.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:44.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:44.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:44.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.590][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.603][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:44.605][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:44.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.610][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:44.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:44.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.622][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:44.624][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:44.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.628][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.631][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:44.633][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.638][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.641][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:44.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.666][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:44.675][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:44.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.679][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:44.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.691][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:44.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:44.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.697][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:44.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.710][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:44.712][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:44.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.717][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.719][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:44.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.728][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:44.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:44.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.735][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.738][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:44.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:44.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:44.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:44.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:44.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:44.839][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-03-02 00:49:44.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:44.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:44.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:44.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:44.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:44.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:44.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:44.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:44.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:44.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:44.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:44.904][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-03-02 00:49:44.906][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:44.910][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-03-02 00:49:44.912][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:44.915][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:44.917][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:44.919][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:44.921][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:44.923][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:44.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:44.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:44.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:44.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:44.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:44.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:44.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:44.945][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-03-02 00:49:44.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:44.951][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:44.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-03-02 00:49:45.332][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-03-02 00:49:45.721][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:45.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-03-02 00:49:46.205][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-03-02 00:49:46.689][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-03-02 00:49:47.182][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:47.185][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:47.187][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:47.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:47.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:47.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:47.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:47.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:47.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:47.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:47.245][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.248][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.255][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.266][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:47.269][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:47.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.274][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:47.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:47.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.286][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:47.288][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:47.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.291][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:47.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:47.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:47.331][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:47.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.336][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:47.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:47.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:47.350][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:47.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.355][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:47.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:47.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.369][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:47.372][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:47.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.378][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.381][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:47.383][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.388][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:47.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.423][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:47.426][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:47.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.430][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:47.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:47.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.443][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:47.445][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:47.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.449][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:47.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:47.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.460][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:47.463][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:47.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.467][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.469][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:47.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:47.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:47.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:47.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.483][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:47.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:47.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:47.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:47.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:47.639][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-03-02 00:49:47.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:47.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:47.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:47.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:47.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:47.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:47.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:47.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:47.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:47.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:47.696][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-03-02 00:49:47.698][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:47.702][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-03-02 00:49:47.719][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:47.722][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:47.724][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:47.727][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:47.730][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:47.732][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:47.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:47.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:47.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:47.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:47.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:47.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:47.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:47.764][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-03-02 00:49:47.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:47.773][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:47.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-03-02 00:49:48.151][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-03-02 00:49:48.542][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:48.546][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-03-02 00:49:49.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-03-02 00:49:49.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-03-02 00:49:49.464][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:49.481][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:49.484][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:49.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:49.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:49.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:49.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:49.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:49.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:49.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:49.516][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.518][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.535][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:49.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:49.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.539][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.542][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:49.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.551][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:49.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:49.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.558][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.581][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:49.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:49.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.603][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.616][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:49.618][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:49.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.622][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:49.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:49.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.631][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:49.633][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:49.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.660][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.663][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:49.665][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.669][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.671][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:49.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:49.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.686][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:49.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:49.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.696][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:49.699][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:49.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.702][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:49.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:49.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.711][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:49.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:49.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.717][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.719][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:49.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:49.728][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:49.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.742][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.745][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:49.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:49.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:49.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:49.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:49.858][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-03-02 00:49:49.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:49.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:49.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:49.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:49.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:49.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:49.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:49.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:49.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:49.921][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-03-02 00:49:49.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:49.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-03-02 00:49:49.929][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:49.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:49.941][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:49.944][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:49.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:49.948][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:49.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:49.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:49.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:49.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:49.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:49.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:49.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:49.975][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-03-02 00:49:49.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:49.983][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:49.986][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-03-02 00:49:50.361][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-03-02 00:49:50.745][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:50.750][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-03-02 00:49:51.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-03-02 00:49:51.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-03-02 00:49:51.357][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:51.360][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:51.363][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:51.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:51.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:51.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:51.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:51.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:51.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:51.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:51.406][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:51.409][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:51.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.430][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.480][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:51.483][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:51.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.487][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:51.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:51.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.499][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:51.501][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:51.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.505][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:51.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.518][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:51.520][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:51.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.551][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:51.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:51.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.591][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:51.593][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:51.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.597][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.624][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:51.627][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:51.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.650][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.653][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:51.655][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:51.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.697][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.701][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:51.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:51.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.718][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:51.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:51.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.733][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:51.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:51.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.750][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:51.753][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:51.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.758][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:51.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:51.781][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:51.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.786][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:51.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:51.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.846][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:51.878][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:51.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.905][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.909][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:51.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:51.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:51.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:51.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:51.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:51.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:51.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:51.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:51.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:52.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:52.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:52.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:52.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:52.178][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-03-02 00:49:52.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:52.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:52.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:52.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:52.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:52.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:52.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:52.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:52.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:52.365][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-03-02 00:49:52.368][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:52.372][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-03-02 00:49:52.376][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:52.378][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:52.381][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:52.390][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:52.394][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:52.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:52.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:52.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:52.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:52.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:52.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:52.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:52.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:52.512][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-03-02 00:49:52.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:52.554][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:52.558][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-03-02 00:49:52.961][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-03-02 00:49:53.373][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:53.377][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-03-02 00:49:53.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-03-02 00:49:53.506][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-03-02 00:49:53.746][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:53.749][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:53.752][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:53.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:53.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:53.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:53.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:53.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:53.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:53.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:53.781][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:53.796][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:53.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.801][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:53.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:53.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.813][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:53.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:53.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.819][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.855][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:53.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.864][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:53.866][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:53.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.871][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:53.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:53.884][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:53.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.888][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.891][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:53.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:53.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.897][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.900][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:53.902][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:53.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.906][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.909][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:53.911][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:53.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.917][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.920][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:53.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:53.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:53.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.975][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:53.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:53.986][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:53.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:53.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:53.993][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:54.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.026][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:54.030][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:54.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.087][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:54.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:54.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.111][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:54.114][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:54.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.118][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:54.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:54.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:54.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:54.317][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-03-02 00:49:54.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:54.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:54.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:54.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:54.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:54.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:54.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:54.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:54.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:54.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:54.452][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-03-02 00:49:54.454][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:54.458][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-03-02 00:49:54.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:54.509][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:54.512][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:54.515][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:54.518][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:54.520][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:54.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:54.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:54.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:54.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:54.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:54.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:54.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:54.574][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-03-02 00:49:54.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:54.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:54.630][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-03-02 00:49:55.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-03-02 00:49:55.442][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:55.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-03-02 00:49:55.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-03-02 00:49:55.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-03-02 00:49:55.990][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:55.993][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:55.996][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:55.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:56.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:56.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:56.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:56.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:56.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:56.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:49:56.025][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.027][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.033][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.046][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:56.049][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:56.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.054][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.059][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:56.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:56.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.071][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:56.073][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:56.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.086][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:56.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:56.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.113][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:56.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:56.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.119][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:56.124][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:56.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.128][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.130][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:56.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:56.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.137][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.139][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:56.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.181][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:56.207][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:56.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.222][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:56.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:56.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.242][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:56.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:56.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.249][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:56.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:56.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:56.297][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:56.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.302][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.305][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.335][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:56.337][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:56.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.341][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:56.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:56.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:56.641][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-03-02 00:49:56.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:56.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:56.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:56.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:56.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:56.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:56.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:56.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:56.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:56.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:56.785][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-03-02 00:49:56.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:56.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-03-02 00:49:56.805][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:56.807][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:56.809][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:56.848][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:56.861][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:56.863][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:56.869][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:56.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:56.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:56.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:56.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:56.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:56.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:56.919][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-03-02 00:49:56.960][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:56.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:56.981][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-03-02 00:49:57.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-03-02 00:49:57.753][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:49:57.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-03-02 00:49:58.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-03-02 00:49:58.419][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-03-02 00:49:58.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:49:58.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:49:58.832][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:49:58.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:58.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:58.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:58.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:58.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:58.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:58.882][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[2024-03-02 00:49:58.888][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:58.891][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:58.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.895][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:58.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:58.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.906][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:58.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:58.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.912][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.915][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:49:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:49:58.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.945][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:58.947][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:58.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.952][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:49:58.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:49:58.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.964][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:58.966][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:58.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.970][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:49:58.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:49:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.981][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:58.984][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:58.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.988][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:49:58.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:49:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:58.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:58.999][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:59.001][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:49:59.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.005][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.008][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:59.010][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.014][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.017][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:49:59.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.027][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:59.029][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:59.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.033][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:59.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:49:59.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.061][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:59.063][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:59.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.085][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:49:59.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:49:59.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.133][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:59.146][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:59.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.150][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:49:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:49:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:59.190][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:59.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.207][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.210][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:49:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:49:59.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:49:59.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:49:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:49:59.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:59.436][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-03-02 00:49:59.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:49:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:49:59.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:49:59.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:49:59.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:59.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:59.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:59.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:59.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:59.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:59.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:59.531][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-03-02 00:49:59.533][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:49:59.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-03-02 00:49:59.556][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:49:59.558][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:49:59.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:49:59.579][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:49:59.588][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:49:59.590][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:49:59.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:49:59.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:49:59.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:49:59.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:49:59.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:49:59.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:49:59.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:49:59.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-03-02 00:49:59.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:49:59.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:49:59.683][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-03-02 00:50:00.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-03-02 00:50:00.443][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:00.447][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-03-02 00:50:00.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-03-02 00:50:00.740][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-03-02 00:50:00.865][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:00.868][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:00.870][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:00.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:00.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:00.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:00.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:00.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:00.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:00.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:00.920][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:00.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:00.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.926][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:00.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:00.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.937][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:00.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:00.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.944][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:00.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:00.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.955][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:00.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:00.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.962][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.967][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:00.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:00.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.978][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:00.980][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:00.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.984][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:00.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:00.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:00.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:00.995][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:00.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:00.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.001][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:01.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:01.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.012][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:01.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:01.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.029][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.039][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:01.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.052][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.054][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:01.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.071][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:01.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:01.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.089][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:01.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.106][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:01.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:01.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.114][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:01.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:01.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:01.134][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:01.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.155][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.158][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:01.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:01.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.177][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:01.180][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:01.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.185][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.198][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:01.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:01.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:01.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:01.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:01.423][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-03-02 00:50:01.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:01.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:01.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:01.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:01.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:01.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:01.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:01.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:01.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:01.507][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-03-02 00:50:01.509][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:01.523][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-03-02 00:50:01.526][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:01.531][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:01.555][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:01.559][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:01.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:01.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:01.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:01.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:01.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:01.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:01.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:01.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:01.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:01.657][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-03-02 00:50:01.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:01.677][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:01.689][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-03-02 00:50:02.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-03-02 00:50:02.477][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:02.481][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-03-02 00:50:02.625][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-03-02 00:50:02.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-03-02 00:50:02.755][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:02.758][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:02.761][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:02.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:02.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:02.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:02.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:02.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:02.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:02.812][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[2024-03-02 00:50:02.816][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:02.818][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:02.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.822][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:02.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:02.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.833][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:02.836][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:02.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.840][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:02.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:02.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.856][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:02.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:02.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.862][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:02.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:02.876][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:02.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.880][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:02.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.891][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:02.894][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:02.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:02.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:02.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:02.913][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:02.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.921][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.923][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:02.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:02.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.930][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.932][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:02.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.942][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:02.944][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:02.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.948][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:02.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:02.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:02.982][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:02.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:02.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:02.989][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:03.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:03.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.022][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:03.025][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:03.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.029][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.044][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:03.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.066][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:03.069][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:03.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.073][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.085][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:03.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:03.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:03.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:03.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:03.351][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-03-02 00:50:03.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:03.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:03.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:03.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:03.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:03.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:03.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:03.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:03.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:03.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:03.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:03.476][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-03-02 00:50:03.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:03.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-03-02 00:50:03.835][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:03.838][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:03.841][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:03.843][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:03.846][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:03.848][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:03.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:03.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:03.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:03.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:03.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:03.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:03.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:03.886][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-03-02 00:50:03.896][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:03.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:03.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-03-02 00:50:04.283][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-03-02 00:50:04.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:04.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-03-02 00:50:04.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-03-02 00:50:05.038][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-03-02 00:50:05.246][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:05.249][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:05.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:05.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:05.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:05.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:05.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:05.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:05.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:05.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:05.282][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.284][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.288][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.301][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:05.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:05.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.311][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.314][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:05.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.336][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:05.338][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:05.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.342][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:05.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:05.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.354][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:05.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:05.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.360][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:05.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:05.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.371][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:05.373][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:05.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.377][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:05.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:05.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.395][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:05.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:05.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.402][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.404][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:05.406][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.410][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.413][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:05.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.421][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:05.423][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:05.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.438][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:05.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:05.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.451][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:05.453][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:05.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.457][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:05.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.495][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:05.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:05.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.504][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.506][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:05.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:05.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.525][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:05.528][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:05.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.545][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.547][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:05.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:05.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:05.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:05.754][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-03-02 00:50:05.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:05.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:05.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:05.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:05.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:05.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:05.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:05.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:05.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:05.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:05.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:05.893][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-03-02 00:50:05.895][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:05.909][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-03-02 00:50:05.912][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:05.914][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:05.916][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:05.918][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:05.921][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:05.934][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:05.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:05.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:05.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:05.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:05.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:05.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:05.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:05.981][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-03-02 00:50:05.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:06.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:06.010][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-03-02 00:50:06.422][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-03-02 00:50:06.807][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:06.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-03-02 00:50:06.823][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-03-02 00:50:06.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-03-02 00:50:07.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:07.112][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:07.115][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:07.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:07.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:07.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:07.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:07.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:07.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:07.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:07.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.151][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.164][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:07.166][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:07.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.170][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.173][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:07.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:07.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.182][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:07.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:07.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.193][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:07.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.204][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:07.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:07.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.210][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:07.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.221][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:07.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:07.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.227][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:07.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.244][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:07.246][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:07.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.250][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.253][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:07.255][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.260][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:07.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.293][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:07.297][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:07.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.301][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:07.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:07.354][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:07.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.358][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:07.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:07.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.386][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:07.388][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:07.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.392][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.412][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:07.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:07.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.422][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:07.425][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:07.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.430][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.448][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:07.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:07.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:07.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:07.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:07.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:07.662][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-03-02 00:50:07.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:07.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:07.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:07.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:07.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:07.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:07.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:07.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:07.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:07.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:07.785][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-03-02 00:50:07.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:07.800][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-03-02 00:50:07.803][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:07.805][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:07.807][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:07.821][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:07.825][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:07.827][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:07.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:07.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:07.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:07.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:07.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:07.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:07.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:07.893][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-03-02 00:50:07.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:07.908][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:07.912][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-03-02 00:50:08.290][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-03-02 00:50:08.672][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:08.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-03-02 00:50:09.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-03-02 00:50:09.322][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-03-02 00:50:09.327][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:09.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:09.333][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:09.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:09.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:09.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:09.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:09.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:09.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:09.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:09.363][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.365][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.370][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.381][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:09.384][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:09.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.388][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:09.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:09.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.404][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:09.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:09.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.410][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:09.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.423][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:09.425][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:09.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.430][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:09.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:09.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:09.452][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:09.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.457][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:09.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:09.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:09.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:09.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.478][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.481][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:09.483][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.487][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.490][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:09.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:09.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:09.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.513][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:09.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:09.550][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:09.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.554][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:09.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:09.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.576][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:09.579][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:09.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.583][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.593][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:09.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:09.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:09.612][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:09.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.616][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:09.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:09.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:09.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:09.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:09.845][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-03-02 00:50:09.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:09.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:09.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:09.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:09.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:09.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:09.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:09.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:09.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:09.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:09.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:09.987][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-03-02 00:50:09.990][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:10.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-03-02 00:50:10.006][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:10.009][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:10.012][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:10.014][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:10.017][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:10.019][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:10.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:10.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:10.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:10.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:10.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:10.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:10.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:10.091][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-03-02 00:50:10.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:10.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:10.111][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-03-02 00:50:10.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-03-02 00:50:10.903][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:10.907][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-03-02 00:50:11.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-03-02 00:50:11.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-03-02 00:50:11.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:11.245][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:11.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:11.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:11.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:11.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:11.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:11.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:11.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:11.272][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[2024-03-02 00:50:11.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.284][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.288][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.301][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:11.304][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:11.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.324][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:11.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.337][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:11.340][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:11.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.344][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:11.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:11.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.356][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:11.359][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:11.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.368][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:11.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.395][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:11.398][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:11.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.403][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:11.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.415][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:11.417][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:11.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.428][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.431][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:11.434][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.439][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.442][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:11.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.458][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:11.471][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:11.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.479][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:11.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.502][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:11.505][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:11.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.544][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:11.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:11.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.556][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:11.559][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:11.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.562][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:11.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:11.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.578][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:11.581][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:11.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.585][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:11.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:11.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:11.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:11.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:11.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:11.804][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-03-02 00:50:11.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:11.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:11.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:11.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:11.964][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:11.980][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:11.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:50:11.987][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:11.990][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-02 00:50:11.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:12.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:12.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:12.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:12.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:12.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:12.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:12.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:12.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:12.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:12.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:12.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:13.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:13.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:13.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:13.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:13.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:13.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:13.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:13.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:13.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:14.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:14.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:14.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:14.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:14.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:14.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:14.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:14.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:14.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:14.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:14.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:14.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:14.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:14.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:14.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:14.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:14.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:14.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:14.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:14.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:14.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:14.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:14.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:14.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:14.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:14.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:14.952][private$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[2024-03-02 00:50:15.358][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[2024-03-02 00:50:15.741][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:15.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-03-02 00:50:15.929][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-03-02 00:50:16.020][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:16.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:16.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:16.035][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-02 00:50:16.419][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-02 00:50:16.798][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:16.803][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-03-02 00:50:16.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-03-02 00:50:16.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:16.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:16.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:16.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:16.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:16.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:16.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:16.889][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-03-02 00:50:16.892][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:16.895][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-03-02 00:50:16.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:16.901][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:16.903][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:16.906][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:16.908][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:16.911][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:16.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:16.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:16.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:16.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:16.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:16.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:16.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:16.941][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-03-02 00:50:16.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:16.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:16.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-03-02 00:50:17.339][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-03-02 00:50:17.731][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:17.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-03-02 00:50:17.755][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-03-02 00:50:17.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-03-02 00:50:17.768][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:17.771][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:17.774][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:17.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:17.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:17.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:17.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:17.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:17.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:17.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:17.839][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:17.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:17.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.847][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:17.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:17.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.862][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:17.864][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:17.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.870][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:17.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:17.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.922][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:17.938][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:17.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.944][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:17.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:17.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:17.980][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:17.983][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:17.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.013][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:18.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:18.058][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:18.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.075][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:18.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.104][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:18.118][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:18.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.124][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:18.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.148][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:18.151][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:18.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.156][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.169][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:18.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.196][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.214][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.242][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:18.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:18.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.264][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:18.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.308][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:18.311][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:18.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.325][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:18.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.349][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:18.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:18.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.371][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.375][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:18.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:18.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:18.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:18.750][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-03-02 00:50:18.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:18.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:18.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:18.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:18.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:18.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:18.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:18.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:18.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:18.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:18.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:18.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:19.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:19.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:19.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:19.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:19.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:19.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:19.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:19.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:19.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:19.084][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-03-02 00:50:19.116][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:19.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-03-02 00:50:19.130][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:19.132][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:19.148][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:19.151][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:19.154][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:19.165][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:19.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:19.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:19.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:19.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:19.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:19.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:19.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:19.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-03-02 00:50:19.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:19.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:19.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-03-02 00:50:19.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-03-02 00:50:20.057][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:20.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-03-02 00:50:20.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-03-02 00:50:20.076][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-03-02 00:50:20.079][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:20.082][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:20.084][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:20.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:20.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:20.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:20.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:20.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:20.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:20.108][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.TRACE[2024-03-02 00:50:20.113][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.115][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.121][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.136][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:20.138][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:20.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.156][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.159][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.177][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:20.179][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:20.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.183][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:20.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:20.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:20.229][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:20.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.234][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:20.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:20.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.262][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:20.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:20.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.287][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:20.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:20.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.322][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:20.325][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:20.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.347][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.350][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:20.369][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:20.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.373][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.376][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:20.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.400][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.421][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.444][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:20.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:20.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.461][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:20.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:20.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.504][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:20.507][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:20.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.526][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.529][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:20.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:20.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.569][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:20.571][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:20.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.587][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:20.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:20.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:20.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:20.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:20.837][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-03-02 00:50:20.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:20.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.039][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:21.058][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:21.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:50:21.064][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:21.066][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-02 00:50:21.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:21.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:21.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:21.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:21.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:21.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:21.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:21.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:21.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:21.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:21.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:21.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:22.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:22.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:22.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:22.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:22.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:22.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:22.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:22.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:22.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:22.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:22.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:23.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:23.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:23.876][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:23.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:23.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-02 00:50:23.906][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:23.925][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-02 00:50:23.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:23.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:23.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:23.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:23.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:23.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:23.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:23.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:24.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:24.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:24.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:24.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:24.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:24.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:24.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:24.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:24.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:25.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:25.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:25.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:25.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:25.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:25.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:25.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:25.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:25.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:25.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:25.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:26.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:26.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:26.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:26.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:26.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:26.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:26.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:26.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:26.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:26.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.638][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:26.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:26.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:50:26.702][biodb::testThat]
biodb.INFO [2024-03-02 00:50:26.705][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-02 00:50:26.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:26.710][biodb::testThat]
biodb.TRACE[2024-03-02 00:50:26.755][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:50:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:50:26.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:26.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:26.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:26.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:26.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:26.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:26.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:26.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:26.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:26.937][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:26.957][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:26.961][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-02 00:50:26.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:26.977][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-02 00:50:26.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:26.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:26.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:27.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:27.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:27.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:27.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:27.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:27.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:27.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:27.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-02 00:50:27.128][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:27.144][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-02 00:50:27.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:27.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:27.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:27.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:27.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:27.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:27.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:27.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:27.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:27.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:27.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:27.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:27.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:27.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:27.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:27.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:27.424][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:27.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:27.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:27.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:27.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:27.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:27.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:27.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:27.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.541][private$selectFields]
biodb.TRACE[2024-03-02 00:50:27.543][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:27.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:27.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.569][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.588][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.603][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.606][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.608][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.610][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.627][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.629][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:27.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.746][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-02 00:50:27.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:27.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:27.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:27.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:27.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:27.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:27.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:27.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.850][private$selectFields]
biodb.TRACE[2024-03-02 00:50:27.864][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:27.866][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:27.868][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.873][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.887][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.892][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.909][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.915][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.918][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.936][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:27.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:27.958][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:27.961][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:27.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.537][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:28.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:28.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:28.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:28.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:28.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:28.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:28.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:28.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.680][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:28.684][private$selectFields]
biodb.TRACE[2024-03-02 00:50:28.687][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:28.702][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:28.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:28.710][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.714][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.731][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.734][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.749][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.754][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:28.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:28.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.781][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.799][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.801][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:28.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:28.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.881][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-02 00:50:28.883][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:28.898][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:29.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:29.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:29.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:29.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:29.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:29.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:29.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:29.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:29.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:29.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:29.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:29.461][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:29.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:29.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:29.504][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-02 00:50:30.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-02 00:50:30.406][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:30.410][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-03-02 00:50:30.421][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-03-02 00:50:30.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:30.438][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:30.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:30.446][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-02 00:50:30.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-02 00:50:31.222][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:31.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-03-02 00:50:31.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-03-02 00:50:31.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:31.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:31.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:31.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:31.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:31.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:31.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:31.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:31.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:31.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:31.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:31.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:31.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:31.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:31.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:31.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:31.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:31.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:31.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:31.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:31.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:31.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:31.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:31.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:31.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:31.722][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:31.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:31.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:31.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:31.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:31.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:31.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:31.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:31.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:31.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:31.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.033][private$selectFields]
biodb.TRACE[2024-03-02 00:50:32.037][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:32.039][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:32.041][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.058][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.064][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.080][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.087][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.100][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.103][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.108][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.124][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.127][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:32.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.198][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-02 00:50:32.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:32.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:32.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:32.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:32.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:32.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:32.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:32.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.500][private$selectFields]
biodb.TRACE[2024-03-02 00:50:32.517][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:32.519][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:32.522][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.548][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.566][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.574][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.645][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.647][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.663][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.669][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.672][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:32.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.763][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:32.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:32.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:32.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:32.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:32.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:32.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:32.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:32.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.861][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.877][private$selectFields]
biodb.TRACE[2024-03-02 00:50:32.880][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:32.882][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:32.885][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.900][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.921][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.927][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.945][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.951][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:32.966][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:32.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:32.987][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:32.990][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:32.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.084][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-02 00:50:33.087][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:33.089][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:33.151][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:33.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:33.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:50:33.197][biodb::testThat]
biodb.INFO [2024-03-02 00:50:33.200][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-02 00:50:33.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:33.217][biodb::testThat]
biodb.TRACE[2024-03-02 00:50:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:50:33.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:50:33.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:33.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:33.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:33.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:33.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:33.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:33.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:33.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:33.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:33.436][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:33.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-02 00:50:33.442][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:33.445][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-02 00:50:33.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:33.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:33.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:33.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:33.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:33.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:33.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:33.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:33.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:33.597][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:33.613][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-02 00:50:33.617][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:33.622][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-02 00:50:33.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:33.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:33.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:33.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:33.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:33.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:33.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:33.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:33.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:33.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:33.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:33.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:33.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:33.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:33.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:33.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:33.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:33.912][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:33.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:33.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:33.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:33.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:33.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:33.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:33.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:33.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:33.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:33.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:33.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.024][private$selectFields]
biodb.TRACE[2024-03-02 00:50:34.027][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:34.043][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:34.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.048][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.064][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.086][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.090][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.092][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.109][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.112][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:34.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.193][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-02 00:50:34.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:34.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:34.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:34.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:34.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:34.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:34.243][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.TRACE[2024-03-02 00:50:34.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.292][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.295][private$selectFields]
biodb.TRACE[2024-03-02 00:50:34.309][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:34.312][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:34.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.317][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.339][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.342][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.354][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.359][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.361][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.363][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.384][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.390][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.406][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.473][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:34.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:34.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:34.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:34.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:34.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:34.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:34.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:34.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.589][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.591][private$selectFields]
biodb.TRACE[2024-03-02 00:50:34.594][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:34.597][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:34.612][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.614][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.644][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.647][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.668][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.674][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:34.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.697][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.699][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:34.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:34.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.787][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-02 00:50:34.790][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:34.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:34.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:34.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:34.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:34.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:34.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:34.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:34.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:34.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:35.012][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:35.032][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:35.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-02 00:50:35.051][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:35.054][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-02 00:50:35.072][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:35.092][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:35.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-02 00:50:35.099][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:35.113][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-02 00:50:35.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:35.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:35.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:35.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:35.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:35.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:35.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:35.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:35.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:35.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:35.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:35.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:35.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:35.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:35.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:35.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:35.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:35.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:35.475][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:35.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:35.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:35.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:35.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:35.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.593][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.595][private$selectFields]
biodb.TRACE[2024-03-02 00:50:35.597][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:35.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:35.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.634][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.655][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.657][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.660][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.662][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.701][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.703][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:35.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.774][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-02 00:50:35.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:35.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:35.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:35.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:35.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:35.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:35.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:35.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.892][private$selectFields]
biodb.TRACE[2024-03-02 00:50:35.912][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:35.914][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:35.916][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.919][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.939][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.961][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:35.963][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.965][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:35.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:35.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:35.989][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.003][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:36.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.088][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:36.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:36.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:36.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:36.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:36.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:36.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:36.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:36.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:36.204][private$selectFields]
biodb.TRACE[2024-03-02 00:50:36.206][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:36.209][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:36.211][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:36.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.235][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.249][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.259][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.261][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:36.275][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:36.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.280][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.298][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:36.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:36.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.373][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-02 00:50:36.375][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:36.392][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:36.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:36.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:50:36.487][biodb::testThat]
biodb.INFO [2024-03-02 00:50:36.489][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-02 00:50:36.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:36.493][biodb::testThat]
biodb.TRACE[2024-03-02 00:50:36.513][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-02 00:50:36.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-02 00:50:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:36.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:36.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:36.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:36.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:36.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:36.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:36.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:36.720][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:36.743][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:36.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-02 00:50:36.750][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:36.768][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-02 00:50:36.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:36.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:36.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:36.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:36.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:36.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:36.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:36.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:36.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:36.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:36.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:36.944][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:36.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-02 00:50:36.950][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:36.964][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-02 00:50:36.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:36.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:36.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:37.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:37.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:37.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:37.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:37.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:37.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:37.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:37.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:37.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:37.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:37.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:37.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:37.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:37.227][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:37.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:37.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:37.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:37.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:37.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:37.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:37.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:37.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.342][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.345][private$selectFields]
biodb.TRACE[2024-03-02 00:50:37.347][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:37.350][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:37.367][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.370][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.389][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.394][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.411][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.415][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.420][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.437][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.439][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:37.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.516][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-02 00:50:37.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:37.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:37.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:37.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:37.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:37.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:37.580][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.TRACE[2024-03-02 00:50:37.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.662][private$selectFields]
biodb.TRACE[2024-03-02 00:50:37.664][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:37.667][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:37.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.686][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.694][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.707][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.714][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.731][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.733][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.740][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.762][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.765][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:37.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.837][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:37.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:37.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:37.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:37.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:37.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:37.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:37.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:37.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.945][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.960][private$selectFields]
biodb.TRACE[2024-03-02 00:50:37.963][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:37.965][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:37.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:37.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.984][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:37.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:37.989][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:37.991][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.011][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:38.026][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:38.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.032][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.048][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:38.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:38.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.125][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-02 00:50:38.127][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:38.129][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:38.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:38.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:38.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:38.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:38.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:38.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:38.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:38.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:38.429][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:38.450][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:38.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-02 00:50:38.469][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:38.472][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-02 00:50:38.489][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:38.505][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:38.508][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-02 00:50:38.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:38.530][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-02 00:50:38.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:38.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:38.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:38.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:38.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:38.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:38.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:38.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:38.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:38.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:38.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:38.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:38.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:38.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:38.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:38.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:38.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:38.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:38.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:38.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:38.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:38.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:38.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:38.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:38.946][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-02 00:50:38.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:38.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:38.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:38.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:38.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:39.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:39.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:39.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.080][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.083][private$selectFields]
biodb.TRACE[2024-03-02 00:50:39.085][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:39.100][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:39.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.108][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.132][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.152][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.158][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.172][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.175][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.197][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.200][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:39.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.296][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-02 00:50:39.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:39.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:39.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:39.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:39.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:39.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:39.375][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.TRACE[2024-03-02 00:50:39.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.444][private$selectFields]
biodb.TRACE[2024-03-02 00:50:39.447][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:39.449][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:39.463][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.466][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.486][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.489][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.511][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.514][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.530][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.562][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.581][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:39.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.660][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-02 00:50:39.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:39.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:39.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:39.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:39.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:39.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:39.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:39.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.788][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.791][private$selectFields]
biodb.TRACE[2024-03-02 00:50:39.793][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-02 00:50:39.803][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-02 00:50:39.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.808][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.811][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.827][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.829][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.832][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.844][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.850][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-02 00:50:39.861][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.868][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.878][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-02 00:50:39.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:39.931][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-02 00:50:39.932][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-02 00:50:39.933][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-02 00:50:39.968][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:39.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-02 00:50:39.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:39.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 00:50:39.982][biodb::testThat]
biodb.INFO [2024-03-02 00:50:39.993][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-02 00:50:39.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:39.999][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:40.002][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-02 00:50:40.012][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:40.016][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-02 00:50:40.019][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-02 00:50:40.031][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 00:50:40.038][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:40.040][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:40.062][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 00:50:40.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 00:50:40.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:40.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:40.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:40.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:40.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:40.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:40.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:40.173][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-03-02 00:50:40.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 00:50:40.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 00:50:40.200][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-03-02 00:50:40.601][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-03-02 00:50:40.994][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 00:50:40.996][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-03-02 00:50:41.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-03-02 00:50:41.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-03-02 00:50:41.010][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 00:50:41.012][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:41.014][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:41.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:41.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:41.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:41.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:41.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:41.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:41.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:41.041][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.045][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.068][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.071][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.083][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.099][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.102][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.106][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:41.114][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:41.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.117][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.120][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.131][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.138][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.145][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.147][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.152][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.154][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:41.156][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:41.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.161][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.162][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.164][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.166][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.168][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:41.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:41.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.184][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.186][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:41.187][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:41.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.189][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:41.199][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:41.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.204][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:41.315][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-03-02 00:50:41.316][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-02 00:50:41.329][biodb::testThat]
biodb.INFO [2024-03-02 00:50:41.330][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-02 00:50:41.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:41.344][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:41.360][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-03-02 00:50:41.362][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-03-02 00:50:41.363][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-03-02 00:50:41.368][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-03-02 00:50:41.370][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-03-02 00:50:41.374][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-03-02 00:50:41.386][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:41.389][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-03-02 00:50:41.391][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:41.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:41.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:41.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:41.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:41.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:41.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:41.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:41.437][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.441][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.457][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.459][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.463][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.468][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.472][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.474][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:41.476][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:41.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.480][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.482][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.486][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.487][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.489][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.491][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.494][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:41.497][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:41.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.516][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.518][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.519][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.522][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.523][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:41.527][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:41.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.531][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.548][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:41.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:41.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.555][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.557][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:41.559][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:41.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.565][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:41.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:41.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:41.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:41.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:41.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:41.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:41.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:41.648][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.649][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.652][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.659][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.660][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.662][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.669][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.670][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.672][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:41.686][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:41.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.688][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:41.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:41.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.708][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:41.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.715][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.716][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.720][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.723][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:41.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.728][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:41.729][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:41.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.732][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.733][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:41.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:41.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.742][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.744][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:41.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.751][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:41.753][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:41.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.755][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:41.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:41.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.763][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:41.765][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:41.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.767][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:41.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.781][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:41.783][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:41.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.786][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:41.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:41.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:41.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:41.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:41.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:41.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:41.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:41.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:41.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:41.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:41.917][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.919][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.922][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:41.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:41.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.937][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.940][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.949][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.956][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.966][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:41.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:41.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:41.976][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:41.979][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:41.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:41.983][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:42.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:42.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.006][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:42.008][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:42.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.017][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:42.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:42.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.050][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:42.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:42.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.056][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.058][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:42.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:42.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.064][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:42.065][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:42.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.072][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.075][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:42.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.124][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.134][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:42.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:42.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.138][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:42.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:42.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:42.157][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:42.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.159][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.160][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:42.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:42.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.166][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:42.167][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:42.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.170][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.182][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:42.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:42.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:42.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:42.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:42.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:42.450][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-03-02 00:50:42.452][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-02 00:50:42.454][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-03-02 00:50:42.494][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.495][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-02 00:50:42.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:42.498][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.549][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.554][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-02 00:50:42.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:42.557][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.568][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.569][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-02 00:50:42.570][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:42.571][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:42.574][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:42.578][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:42.580][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-03-02 00:50:42.581][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:42.593][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-03-02 00:50:42.717][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:42.718][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:42.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.720][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:42.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:42.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:42.725][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 00:50:42.727][biodb::testThat]
biodb.INFO [2024-03-02 00:50:42.729][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-02 00:50:42.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:42.735][biodb::testThat]
biodb.ERROR[2024-03-02 00:50:42.753][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-02 00:50:42.794][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-02 00:50:42.812][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:50:42.813][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-02 00:50:42.822][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-02 00:50:42.824][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:50:42.827][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:42.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:42.839][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:42.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:42.842][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:42.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:50:42.881][biodb::testContext]
biodb.INFO [2024-03-02 00:50:42.886][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:42.893][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-03-02 00:50:42.895][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:42.897][biodb::testContext]
biodb.INFO [2024-03-02 00:50:42.903][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:42.907][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:43.025][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:43.027][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:50:43.029][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.048][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:50:43.050][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.071][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:50:43.073][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.098][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:50:43.111][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:50:43.114][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:50:43.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.138][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:50:43.141][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:50:43.143][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.165][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:50:43.167][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:50:43.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.186][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:50:43.188][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:50:43.190][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:50:43.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.206][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[2024-03-02 00:50:43.208][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:50:43.222][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.230][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:50:43.241][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:50:43.245][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:50:43.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.263][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[2024-03-02 00:50:43.266][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:43.268][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:50:43.270][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:50:43.279][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:50:43.281][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:50:43.284][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:50:43.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.307][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:50:43.309][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:50:43.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.333][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:50:43.336][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:50:43.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.354][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:50:43.356][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:50:43.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.375][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[2024-03-02 00:50:43.377][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:50:43.380][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:50:43.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.398][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:50:43.411][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:50:43.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.418][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[2024-03-02 00:50:43.420][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:43.439][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:50:43.468][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:50:43.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.477][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:50:43.490][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:50:43.492][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:50:43.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.514][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:50:43.518][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.521][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:50:43.541][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.544][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:43.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.549][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.567][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.570][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.572][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:43.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:43.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.594][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:50:43.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:43.598][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.611][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:43.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:43.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:43.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:43.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:43.616][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:43.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.637][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:43.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.657][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:43.661][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:43.663][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.666][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.686][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:50:43.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.693][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:43.702][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:43.707][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.709][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.711][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.715][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:43.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:43.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.721][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:50:43.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:43.725][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.727][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.729][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:43.729][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:43.729][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:43.729][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:43.729][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:43.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:43.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:43.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.744][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.745][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:43.747][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:43.749][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.751][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.754][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:50:43.757][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.759][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:50:43.761][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:43.766][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.774][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:43.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:43.783][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.785][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:50:43.787][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:43.789][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.792][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.794][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:43.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.801][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:43.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.807][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:43.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:43.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.819][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.821][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:50:43.823][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.825][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:43.826][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.832][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:43.835][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.837][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.841][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.844][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:43.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:43.858][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.860][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:50:43.862][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:43.864][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:43.868][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.869][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:43.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:43.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:43.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:43.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:43.878][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.880][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:43.881][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:43.883][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:43.884][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:43.885][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:43.886][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.888][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[2024-03-02 00:50:43.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.927][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[2024-03-02 00:50:43.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:43.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:43.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:43.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:43.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:43.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.102][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[2024-03-02 00:50:44.103][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:50:44.104][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:50:44.107][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:50:44.112][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:50:44.117][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:44.121][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:50:44.134][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:44.137][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:44.141][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:50:44.155][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:50:44.159][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:44.166][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:50:44.170][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:44.173][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:44.181][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:50:44.185][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:50:44.188][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:50:44.199][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:50:44.203][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:44.211][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:50:44.214][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:50:44.217][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:50:44.230][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:50:44.234][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:50:44.237][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:50:44.244][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:50:44.248][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:50:44.251][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:50:44.256][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:50:44.259][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:50:44.262][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:50:44.265][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:50:44.268][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:50:44.271][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:50:44.272][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:50:44.275][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:50:44.277][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:50:44.278][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:50:44.291][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:50:44.307][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:50:44.310][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:50:44.313][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:50:44.319][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:50:44.323][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:50:44.326][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:50:44.329][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:50:44.333][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:50:44.336][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:50:44.339][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:50:44.426][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:50:44.429][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:50:44.432][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:50:44.450][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:50:44.453][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:50:44.456][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:50:44.475][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:50:44.478][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:50:44.481][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:50:44.497][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:50:44.501][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:50:44.504][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:50:44.522][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:50:44.526][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:50:44.529][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:50:44.548][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:50:44.551][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:50:44.555][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:44.573][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:44.576][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:50:44.579][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:50:44.609][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:50:44.613][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:50:44.632][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:50:44.635][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:50:44.638][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:50:44.654][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:50:44.658][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:50:44.661][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:50:44.682][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:50:44.686][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:50:44.689][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:50:44.706][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:50:44.710][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:50:44.714][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:50:44.732][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:44.735][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:44.737][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.756][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.791][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[2024-03-02 00:50:44.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.949][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[2024-03-02 00:50:44.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:44.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:44.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:44.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:44.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:44.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:44.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:44.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.327][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[2024-03-02 00:50:45.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.376][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[2024-03-02 00:50:45.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:45.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.445][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:45.460][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-02 00:50:45.465][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:45.468][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:50:45.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:45.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:45.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:45.493][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:45.495][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:45.509][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-02 00:50:45.511][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-02 00:50:45.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:45.515][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:45.529][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-02 00:50:45.532][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-02 00:50:45.534][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-02 00:50:45.537][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:45.554][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:45.554][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:45.554][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:45.558][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 00:50:45.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:45.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:45.575][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:45.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:45.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:45.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:45.583][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:45.583][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-02 00:50:45.595][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:45.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:45.604][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:45.607][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-02 00:50:45.607][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-02 00:50:45.622][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:45.626][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:45.630][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-02 00:50:45.650][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:45.654][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:45.669][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:45.677][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-02 00:50:45.680][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-02 00:50:45.683][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-02 00:50:45.686][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-02 00:50:45.697][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:45.699][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:45.702][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-02 00:50:45.705][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-02 00:50:45.707][biodb::testThat]
biodb.INFO [2024-03-02 00:50:45.709][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-03-02 00:50:45.711][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:45.714][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:45.719][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-02 00:50:45.729][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-02 00:50:45.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.754][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-02 00:50:45.782][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:45.800][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-02 00:50:45.803][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.805][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-02 00:50:45.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.821][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:45.826][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.827][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-02 00:50:45.829][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.831][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-02 00:50:45.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.910][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:45.917][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-02 00:50:45.922][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.925][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-02 00:50:45.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.942][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:45.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.949][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-02 00:50:45.951][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.953][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-02 00:50:45.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:45.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:45.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:45.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:45.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:45.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:45.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:45.983][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:45.989][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:45.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-02 00:50:45.994][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:45.996][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-02 00:50:45.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:46.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:46.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:46.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-02 00:50:46.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:46.024][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-02 00:50:46.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:46.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:46.046][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:46.047][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-03-02 00:50:46.049][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:46.051][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-03-02 00:50:46.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:46.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:50:46.098][biodb::testThat]
biodb.INFO [2024-03-02 00:50:46.101][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-03-02 00:50:46.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:46.105][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:46.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:46.127][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:46.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-03-02 00:50:46.141][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:46.143][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-03-02 00:50:46.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:46.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.183][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:46.187][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:46.188][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-03-02 00:50:46.190][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:46.205][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-03-02 00:50:46.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:46.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:50:46.360][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:50:46.362][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-02 00:50:46.365][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-02 00:50:46.367][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:50:46.371][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:46.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:46.373][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:46.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:46.376][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:50:46.381][biodb::testContext]
biodb.INFO [2024-03-02 00:50:46.383][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:46.385][biodb::testContext] Test context - Test web services
biodb.INFO [2024-03-02 00:50:46.387][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:46.388][biodb::testContext]
biodb.INFO [2024-03-02 00:50:46.445][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:46.461][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:46.499][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:46.501][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:50:46.502][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.510][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:50:46.513][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.518][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:50:46.519][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.524][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:50:46.526][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:50:46.528][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:50:46.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.542][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:50:46.544][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:50:46.546][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.555][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:50:46.558][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:50:46.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.566][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:50:46.568][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:50:46.570][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:50:46.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.577][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.DEBUG[2024-03-02 00:50:46.579][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:50:46.582][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.595][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:50:46.597][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:50:46.601][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:50:46.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.607][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.DEBUG[2024-03-02 00:50:46.609][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:46.611][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:50:46.614][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:50:46.616][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:50:46.619][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:50:46.621][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:50:46.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.628][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:50:46.630][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:50:46.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.640][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:50:46.646][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:50:46.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.653][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:50:46.654][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:50:46.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.694][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[2024-03-02 00:50:46.696][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:50:46.698][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:50:46.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.735][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:50:46.750][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:50:46.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.765][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:46.777][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:50:46.810][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:50:46.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.818][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:50:46.831][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:50:46.833][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:50:46.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:46.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:46.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:46.852][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:50:46.856][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:46.866][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:50:46.869][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:46.871][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:46.873][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:46.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:46.890][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:46.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:46.895][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:46.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:46.920][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:46.922][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:50:46.924][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:46.926][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:46.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:46.944][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:46.944][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:46.944][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:46.944][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:46.944][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:46.947][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:46.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:46.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:46.966][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:46.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:46.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:46.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:46.988][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:46.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:46.992][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:46.994][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.012][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.015][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:50:47.019][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.037][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:47.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.042][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:47.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.047][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:47.056][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:47.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.090][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:50:47.092][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:47.095][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:47.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:47.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:47.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:47.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:47.114][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:47.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:47.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.166][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:47.171][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:47.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.189][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.192][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:50:47.196][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.210][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:50:47.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:47.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.235][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.237][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.240][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:47.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:47.256][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.264][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:50:47.266][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:47.280][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.283][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.285][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.287][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:47.289][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.306][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:47.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.324][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.327][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.329][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:47.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:47.333][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.346][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.350][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:50:47.355][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.373][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:47.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:47.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.400][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.405][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:47.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:47.424][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.427][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:50:47.429][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:47.432][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.445][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:47.448][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:47.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:47.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:47.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:47.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:47.492][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:47.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:47.499][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:47.514][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:47.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:47.520][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.751][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[2024-03-02 00:50:47.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.800][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[2024-03-02 00:50:47.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:47.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:47.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:47.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:47.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:47.955][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:50:47.958][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:50:47.961][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:50:47.976][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:50:47.979][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:47.983][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:50:47.998][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:48.002][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:48.005][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:50:48.020][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:50:48.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:48.026][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:50:48.043][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:48.046][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:48.049][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:50:48.066][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:50:48.070][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:50:48.086][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:50:48.089][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:48.113][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:50:48.118][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:50:48.134][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:50:48.138][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:50:48.141][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:50:48.157][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:50:48.161][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:50:48.165][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:50:48.181][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:50:48.186][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:50:48.190][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:50:48.205][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:50:48.208][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:50:48.211][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:50:48.228][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:50:48.232][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:50:48.236][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:50:48.256][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:50:48.267][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:50:48.288][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:50:48.293][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:50:48.296][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:50:48.313][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:50:48.317][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:50:48.321][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:50:48.337][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:50:48.341][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:50:48.344][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:50:48.362][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:50:48.365][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:50:48.368][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:50:48.393][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:50:48.397][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:50:48.401][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:50:48.419][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:50:48.422][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:50:48.426][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:50:48.440][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:50:48.443][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:50:48.446][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:50:48.459][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:50:48.463][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:50:48.466][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:50:48.481][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:50:48.484][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:50:48.487][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:50:48.500][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:50:48.504][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:48.507][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:48.526][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:50:48.529][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:50:48.532][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:50:48.548][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:50:48.551][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:50:48.554][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:50:48.571][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:50:48.574][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:50:48.589][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:50:48.593][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:50:48.597][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:50:48.612][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:50:48.615][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:50:48.618][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:50:48.621][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:50:48.637][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:50:48.641][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:48.643][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:48.661][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.665][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:48.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:48.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:48.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:48.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:48.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:48.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:48.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.211][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:49.215][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-02 00:50:49.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:49.235][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:50:49.238][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:49.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:49.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:49.255][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:49.258][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:49.261][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-02 00:50:49.263][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-02 00:50:49.279][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:49.281][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:49.283][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-02 00:50:49.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-02 00:50:49.299][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-02 00:50:49.302][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:49.305][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:49.305][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:49.305][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:49.307][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 00:50:49.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:49.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:49.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:49.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:49.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:49.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:49.348][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:49.348][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-02 00:50:49.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:49.352][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:49.367][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:49.370][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-02 00:50:49.370][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-02 00:50:49.373][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:49.388][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:49.394][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-02 00:50:49.398][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:49.416][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:49.419][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:49.441][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-02 00:50:49.444][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-02 00:50:49.446][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-02 00:50:49.460][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-02 00:50:49.465][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:49.467][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:49.482][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-02 00:50:49.484][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-02 00:50:49.487][biodb::testThat]
biodb.INFO [2024-03-02 00:50:49.490][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-03-02 00:50:49.492][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:49.506][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:49.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-02 00:50:49.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:49.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-02 00:50:49.553][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:49.556][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-02 00:50:49.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:49.599][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:49.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-03-02 00:50:49.617][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:49.631][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-03-02 00:50:49.658][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:50:49.673][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-02 00:50:49.678][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-02 00:50:49.680][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:50:49.682][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:49.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:49.700][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:49.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:49.705][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 00:50:49.738][biodb::testContext]
biodb.INFO [2024-03-02 00:50:49.740][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:49.743][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-03-02 00:50:49.745][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 00:50:49.747][biodb::testContext]
biodb.INFO [2024-03-02 00:50:49.778][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:49.782][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:49.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:49.806][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 00:50:49.808][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 00:50:49.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.828][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 00:50:49.830][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 00:50:49.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.870][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 00:50:49.872][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 00:50:49.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.895][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 00:50:49.897][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 00:50:49.912][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 00:50:49.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.920][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 00:50:49.936][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 00:50:49.939][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 00:50:49.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.958][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 00:50:49.960][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 00:50:49.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:49.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:49.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:49.982][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 00:50:49.984][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 00:50:49.987][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 00:50:50.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.007][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 00:50:50.009][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 00:50:50.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.031][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 00:50:50.047][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 00:50:50.050][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 00:50:50.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.081][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:50.084][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 00:50:50.086][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 00:50:50.088][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 00:50:50.090][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 00:50:50.104][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 00:50:50.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.122][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 00:50:50.124][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 00:50:50.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.144][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 00:50:50.147][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 00:50:50.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.167][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 00:50:50.169][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 00:50:50.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.190][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 00:50:50.192][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 00:50:50.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.212][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 00:50:50.214][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 00:50:50.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.232][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 00:50:50.235][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 00:50:50.280][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 00:50:50.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:50.288][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 00:50:50.301][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 00:50:50.304][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 00:50:50.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:50.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:50.321][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.DEBUG[2024-03-02 00:50:50.323][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 00:50:50.327][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.330][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 00:50:50.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:50.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.368][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:50.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:50.383][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.386][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 00:50:50.388][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:50.394][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.409][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.412][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:50.412][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:50.412][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:50.412][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:50.412][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:50.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:50.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:50.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.455][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:50.459][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:50.461][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.474][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.477][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 00:50:50.481][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.484][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:50.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.502][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:50.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.509][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.526][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:50.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:50.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.544][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 00:50:50.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:50.549][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.562][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.564][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:50.564][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:50.564][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:50.564][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 00:50:50.564][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 00:50:50.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:50.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:50.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.606][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.608][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:50.610][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:50.612][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.626][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.631][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 00:50:50.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.653][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 00:50:50.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:50.660][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.676][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.679][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.684][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 00:50:50.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:50.700][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.703][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 00:50:50.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:50.719][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.721][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.724][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.726][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:50.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:50.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.765][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.768][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:50.786][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:50.789][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.791][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.807][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 00:50:50.811][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 00:50:50.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:50.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.857][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.881][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.885][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.888][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 00:50:50.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:50.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.905][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 00:50:50.907][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:50.919][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:50.924][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 00:50:50.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:50.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:50.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:50.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:50.979][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:50.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:50.994][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:50.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:50.999][self$setPropertyValue]
biodb.DEBUG[2024-03-02 00:50:51.012][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:51.015][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.157][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[2024-03-02 00:50:51.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.194][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[2024-03-02 00:50:51.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.242][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[2024-03-02 00:50:51.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.378][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[2024-03-02 00:50:51.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:51.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:51.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:51.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:51.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:51.489][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.DEBUG[2024-03-02 00:50:51.492][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 00:50:51.511][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 00:50:51.516][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 00:50:51.532][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 00:50:51.536][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:51.540][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 00:50:51.557][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:51.562][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:51.575][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 00:50:51.579][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 00:50:51.584][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:51.609][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 00:50:51.613][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 00:50:51.625][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 00:50:51.629][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 00:50:51.633][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 00:50:51.653][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 00:50:51.668][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 00:50:51.674][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:51.688][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 00:50:51.692][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 00:50:51.696][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 00:50:51.713][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 00:50:51.718][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 00:50:51.752][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 00:50:51.768][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 00:50:51.773][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 00:50:51.776][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 00:50:51.793][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 00:50:51.797][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 00:50:51.800][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 00:50:51.816][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 00:50:51.820][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 00:50:51.824][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 00:50:51.838][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 00:50:51.841][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 00:50:51.859][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 00:50:51.863][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 00:50:51.867][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 00:50:51.887][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 00:50:51.891][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 00:50:51.899][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 00:50:51.903][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 00:50:51.907][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 00:50:51.927][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 00:50:51.932][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 00:50:51.941][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 00:50:51.946][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 00:50:51.952][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 00:50:51.979][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 00:50:51.982][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 00:50:51.998][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 00:50:52.002][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 00:50:52.007][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 00:50:52.017][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 00:50:52.022][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 00:50:52.035][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 00:50:52.039][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 00:50:52.053][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 00:50:52.058][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 00:50:52.070][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 00:50:52.075][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 00:50:52.081][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 00:50:52.092][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 00:50:52.097][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 00:50:52.115][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 00:50:52.121][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:52.138][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:52.147][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 00:50:52.166][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 00:50:52.171][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 00:50:52.175][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 00:50:52.193][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 00:50:52.197][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 00:50:52.214][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 00:50:52.218][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 00:50:52.237][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 00:50:52.242][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 00:50:52.246][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 00:50:52.261][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 00:50:52.264][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 00:50:52.281][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 00:50:52.286][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 00:50:52.291][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 00:50:52.307][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-02 00:50:52.310][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 00:50:52.313][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.331][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.334][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[2024-03-02 00:50:52.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.446][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[2024-03-02 00:50:52.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.744][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[2024-03-02 00:50:52.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:52.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:52.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:52.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:52.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:52.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:52.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:52.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:53.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:53.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 00:50:53.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:53.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:53.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:53.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:53.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:53.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 00:50:53.071][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-02 00:50:53.093][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-02 00:50:53.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:53.100][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-02 00:50:53.116][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:53.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 00:50:53.122][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:53.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 00:50:53.138][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:53.140][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-02 00:50:53.143][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-02 00:50:53.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 00:50:53.162][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:53.165][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-02 00:50:53.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-02 00:50:53.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-02 00:50:53.186][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 00:50:53.188][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 00:50:53.188][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 00:50:53.188][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 00:50:53.191][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 00:50:53.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:53.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:53.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 00:50:53.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 00:50:53.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 00:50:53.229][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 00:50:53.233][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-02 00:50:53.233][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-02 00:50:53.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 00:50:53.253][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 00:50:53.255][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 00:50:53.258][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-02 00:50:53.258][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-02 00:50:53.262][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 00:50:53.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 00:50:53.285][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-02 00:50:53.303][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 00:50:53.308][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 00:50:53.312][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 00:50:53.333][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-02 00:50:53.335][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-02 00:50:53.349][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-02 00:50:53.352][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-02 00:50:53.355][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:53.370][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 00:50:53.375][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-02 00:50:53.377][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-02 00:50:53.380][biodb::testThat]
biodb.INFO [2024-03-02 00:50:53.396][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-03-02 00:50:53.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 00:50:53.400][biodb::testThat]
biodb.DEBUG[2024-03-02 00:50:53.423][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-02 00:50:53.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:53.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-02 00:50:53.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:53.471][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-02 00:50:53.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-02 00:50:53.505][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 00:50:53.524][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-03-02 00:50:53.527][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:53.532][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-03-02 00:50:53.644][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-03-02 00:50:53.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-02 00:50:53.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-03-02 00:50:53.670][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 00:50:53.675][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-03-02 00:50:53.689][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 00:50:53.692][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-02 00:50:53.695][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-02 00:50:53.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 00:50:53.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:53.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:53.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:53.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:53.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:53.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 00:50:53.786][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:53.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:53.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.827][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:53.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.856][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:53.858][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:53.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.878][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-02 00:50:53.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-02 00:50:53.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.906][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:53.909][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:53.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.928][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-02 00:50:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-02 00:50:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.951][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-02 00:50:53.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-02 00:50:53.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.968][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-02 00:50:53.974][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-02 00:50:53.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:53.990][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:53.994][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:53.996][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:53.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.013][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-02 00:50:54.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.039][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:54.042][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:54.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.059][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.062][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-02 00:50:54.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-02 00:50:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.084][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:54.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:54.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.103][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:54.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-02 00:50:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:54.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:54.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.145][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 00:50:54.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 00:50:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:54.175][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:54.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.180][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-02 00:50:54.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-02 00:50:54.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.193][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:54.195][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:54.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.207][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.210][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-02 00:50:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-02 00:50:54.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-02 00:50:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 00:50:54.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 00:50:54.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 00:50:54.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 00:50:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 00:50:54.340][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-03-02 00:50:54.354][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 00:50:54.356][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-02 00:50:54.358][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-02 00:50:54.360][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 00:50:54.365][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 00:50:54.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 00:50:54.369][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 00:50:54.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 00:50:54.373][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 00:50:54.374][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 382 ]
>
> proc.time()
user system elapsed
38.369 2.184 101.749
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.654 | 1.461 | 40.609 | |
| ChebiEntry | 0.819 | 0.027 | 1.059 | |