Pierrick Roger
| Snapshot Date: 2024-06-24 14:00 -0400 (Mon, 24 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: dfe3f6c |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-25 11:39 -0400 (Tue, 25 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
| 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 197/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2024-06-24 19:16:54 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 19:17:55 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 60.7 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-arm64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 [2024-06-24 19:17:13.267][biodb::testContext]
biodb.INFO [2024-06-24 19:17:13.268][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:13.269][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-24 19:17:13.269][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:13.269][biodb::testContext]
biodb.INFO [2024-06-24 19:17:13.272][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:13.273][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:13.276][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:13.277][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 19:17:13.277][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.278][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 19:17:13.284][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.285][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[2024-06-24 19:17:13.286][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 19:17:13.286][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.287][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 19:17:13.287][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 19:17:13.288][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 19:17:13.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.294][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 19:17:13.294][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 19:17:13.294][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.295][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 19:17:13.295][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 19:17:13.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.296][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 19:17:13.297][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 19:17:13.297][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 19:17:13.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.298][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 19:17:13.298][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.299][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 19:17:13.299][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 19:17:13.299][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 19:17:13.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.300][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:13.301][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 19:17:13.301][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 19:17:13.301][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 19:17:13.301][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 19:17:13.302][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 19:17:13.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.303][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 19:17:13.303][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 19:17:13.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.304][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 19:17:13.304][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 19:17:13.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.305][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 19:17:13.305][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 19:17:13.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.306][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 19:17:13.306][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 19:17:13.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.307][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 19:17:13.308][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 19:17:13.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.309][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:13.309][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 19:17:13.314][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 19:17:13.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.316][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 19:17:13.316][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 19:17:13.316][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 19:17:13.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.318][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 19:17:13.329][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.333][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 19:17:13.334][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.334][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:13.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.335][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:13.335][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:13.336][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.336][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 19:17:13.336][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:13.336][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:13.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.338][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:13.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.338][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.339][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:13.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:13.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.339][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.340][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 19:17:13.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.340][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:13.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.341][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:13.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.342][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.342][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:13.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:13.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.343][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 19:17:13.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:13.343][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.343][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:13.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:13.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.345][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:13.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:13.346][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.346][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.347][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 19:17:13.347][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.347][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 19:17:13.347][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:13.348][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.348][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.349][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:13.351][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:13.352][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.352][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 19:17:13.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:13.352][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.353][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.353][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:13.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.354][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:13.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.354][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:13.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:13.355][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.355][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.356][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 19:17:13.356][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.356][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:13.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:13.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.357][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.358][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.358][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:13.358][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:13.358][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.359][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 19:17:13.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:13.359][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.359][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.359][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.360][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:13.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:13.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.361][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.361][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:13.362][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:13.362][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.362][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:13.364][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:13.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.375][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[2024-06-24 19:17:13.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.376][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[2024-06-24 19:17:13.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.378][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[2024-06-24 19:17:13.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.382][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 19:17:13.384][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 19:17:13.385][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 19:17:13.385][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 19:17:13.386][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:13.386][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 19:17:13.387][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:13.387][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:13.387][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 19:17:13.388][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 19:17:13.388][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:13.388][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 19:17:13.389][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:13.389][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:13.390][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 19:17:13.390][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 19:17:13.390][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 19:17:13.391][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 19:17:13.391][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:13.391][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 19:17:13.392][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 19:17:13.392][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 19:17:13.392][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 19:17:13.393][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 19:17:13.393][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 19:17:13.394][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 19:17:13.394][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 19:17:13.394][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 19:17:13.395][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 19:17:13.395][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 19:17:13.395][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 19:17:13.396][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 19:17:13.396][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 19:17:13.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 19:17:13.397][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 19:17:13.397][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 19:17:13.398][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 19:17:13.398][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 19:17:13.398][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 19:17:13.399][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 19:17:13.399][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 19:17:13.399][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 19:17:13.400][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 19:17:13.400][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 19:17:13.403][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 19:17:13.403][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 19:17:13.404][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 19:17:13.404][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 19:17:13.404][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 19:17:13.405][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 19:17:13.405][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 19:17:13.405][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 19:17:13.406][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 19:17:13.406][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 19:17:13.407][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 19:17:13.407][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 19:17:13.407][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 19:17:13.408][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 19:17:13.408][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 19:17:13.408][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 19:17:13.409][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 19:17:13.409][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 19:17:13.409][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 19:17:13.410][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 19:17:13.410][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 19:17:13.411][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 19:17:13.411][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:13.411][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:13.412][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 19:17:13.412][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 19:17:13.413][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 19:17:13.413][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 19:17:13.413][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 19:17:13.414][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 19:17:13.414][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 19:17:13.414][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 19:17:13.415][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 19:17:13.415][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 19:17:13.415][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 19:17:13.416][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 19:17:13.416][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 19:17:13.417][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 19:17:13.417][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 19:17:13.419][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 19:17:13.419][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:13.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:13.421][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.422][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.425][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[2024-06-24 19:17:13.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.434][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.DEBUG[2024-06-24 19:17:13.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.437][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[2024-06-24 19:17:13.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.442][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[2024-06-24 19:17:13.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:13.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:13.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.450][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[2024-06-24 19:17:13.450][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:13.456][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 19:17:13.456][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.457][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.457][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.457][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:13.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.458][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.458][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 19:17:13.458][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 19:17:13.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:13.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.459][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 19:17:13.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:13.460][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:13.461][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 19:17:13.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:13.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:13.462][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:13.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:13.462][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:13.462][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 19:17:13.462][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:13.463][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:13.463][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:13.463][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 19:17:13.463][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 19:17:13.465][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:13.466][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:13.466][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 19:17:13.466][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:13.467][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:13.467][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:13.478][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 19:17:13.478][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 19:17:13.480][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 19:17:13.482][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 19:17:13.483][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:13.484][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:13.484][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 19:17:13.484][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 19:17:13.488][biodb::testThat]
biodb.INFO [2024-06-24 19:17:13.488][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-24 19:17:13.489][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:13.489][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:13.491][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-24 19:17:13.492][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:13.493][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:13.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:13.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:13.507][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.508][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.508][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.513][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.514][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.524][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.525][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.530][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.531][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.532][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.533][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.534][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.535][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.536][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.536][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.536][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.538][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:13.538][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.539][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.540][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.540][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.542][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.543][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:13.545][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.545][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.546][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.547][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.547][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:13.570][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-24 19:17:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.597][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:13.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:13.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.598][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:13.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:13.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:13.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:13.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.628][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.629][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.629][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.639][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.639][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.646][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.646][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.646][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.653][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.653][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.654][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.660][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.660][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.661][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.667][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.671][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.672][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.673][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.674][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.676][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.677][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.677][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.680][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.683][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.683][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.683][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.688][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.689][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.690][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.693][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.694][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.696][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.697][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.697][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.704][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.704][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.712][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.712][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.716][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.718][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.722][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.722][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.724][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.725][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.726][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.728][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.728][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.729][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.730][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.730][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.731][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.732][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.733][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.734][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.734][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.736][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.736][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.738][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.738][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.739][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.740][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.740][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.741][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:13.743][biodb::testThat]
biodb.INFO [2024-06-24 19:17:13.743][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-24 19:17:13.743][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:13.744][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:13.748][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-24 19:17:13.751][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:13.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-24 19:17:13.752][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:13.753][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-24 19:17:13.753][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:13.760][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:13.760][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:13.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:13.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:13.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:13.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:13.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:13.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:13.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:13.764][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.765][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.765][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.773][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.773][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.774][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.775][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.776][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:13.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:13.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.779][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:13.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.781][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.781][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.782][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.783][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:13.783][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.784][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.784][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:13.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:13.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.785][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.785][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.787][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.787][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.789][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:13.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.790][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.790][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.791][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.791][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.792][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:13.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:13.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:13.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:13.802][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-24 19:17:13.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-24 19:17:13.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-24 19:17:13.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-24 19:17:13.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-24 19:17:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-24 19:17:13.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-24 19:17:13.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:13.810][biodb::testThat]
biodb.INFO [2024-06-24 19:17:13.811][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-24 19:17:13.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:13.811][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:13.812][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.813][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:13.813][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-24 19:17:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:13.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:13.824][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-24 19:17:13.826][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 19:17:13.832][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:13.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 19:17:13.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:13.838][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 19:17:13.844][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[2024-06-24 19:17:13.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:13.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:13.846][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:14.355][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:14.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:14.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-24 19:17:14.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-24 19:17:14.833][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-24 19:17:14.837][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:14.837][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:14.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.838][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.839][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.844][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:14.846][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.846][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-24 19:17:14.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:14.847][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:14.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:14.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:14.875][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:14.876][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:14.877][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:14.877][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:14.878][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-24 19:17:14.886][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.886][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-24 19:17:14.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:14.886][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:14.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:14.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:14.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:14.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:14.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:14.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.902][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:14.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:14.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:14.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.919][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 19:17:14.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 19:17:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:14.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:14.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 19:17:14.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:14.924][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.925][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-24 19:17:14.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:14.925][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.928][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.928][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-24 19:17:14.928][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:14.928][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.931][biodb::testThat]
biodb.INFO [2024-06-24 19:17:14.931][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-24 19:17:14.931][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:14.932][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:14.933][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-24 19:17:15.401][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-24 19:17:16.411][biodb::testThat]
biodb.INFO [2024-06-24 19:17:16.412][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-24 19:17:16.412][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:16.413][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:16.771][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[2024-06-24 19:17:17.131][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:17.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:17.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.132][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:17.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:17.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.133][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:17.134][biodb::testThat]
biodb.INFO [2024-06-24 19:17:17.134][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-06-24 19:17:17.134][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:17.135][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:17.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:17.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:17.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:17.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:17.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:17.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:17.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:17.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:17.171][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:17.171][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 19:17:17.191][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:17.192][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:17.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:17.193][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:17.193][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-24 19:17:17.197][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 19:17:17.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 19:17:17.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:17.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:17.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:17.207][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:17.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:17.213][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:17.218][private$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[2024-06-24 19:17:17.563][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[2024-06-24 19:17:17.892][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:17.893][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-24 19:17:17.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-24 19:17:17.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:17.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:17.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:17.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:17.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:17.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:17.899][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[2024-06-24 19:17:17.899][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-24 19:17:17.915][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:17.915][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-24 19:17:17.916][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:17.916][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:17.916][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:17.917][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:17.917][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:17.917][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:17.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:17.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:17.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:17.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:17.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:17.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:17.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:17.922][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-24 19:17:17.922][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:17.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:17.923][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-24 19:17:18.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-24 19:17:18.587][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:18.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-24 19:17:18.591][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-24 19:17:18.592][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-24 19:17:18.592][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:18.593][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:18.593][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:18.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:18.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:18.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:18.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:18.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:18.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:18.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:18.598][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.598][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.599][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.600][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:18.600][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:18.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.601][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:18.602][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:18.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.603][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.603][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:18.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:18.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:18.605][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:18.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.605][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:18.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.607][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:18.607][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:18.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.607][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.608][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:18.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.609][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:18.609][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:18.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.609][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.610][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:18.610][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.611][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:18.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:18.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:18.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.613][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:18.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.614][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:18.614][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:18.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:18.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.616][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:18.616][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:18.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.617][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.617][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:18.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.618][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:18.619][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:18.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.619][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:18.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:18.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:18.634][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-24 19:17:18.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:18.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:18.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:18.641][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[2024-06-24 19:17:18.642][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:18.642][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:18.643][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:18.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:19.304][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:19.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-24 19:17:19.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-24 19:17:19.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:19.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:19.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:19.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:19.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:19.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:19.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:19.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:19.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:19.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:19.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:19.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:19.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:19.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:19.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:19.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:19.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:19.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:19.326][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-24 19:17:19.326][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:19.326][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-24 19:17:19.327][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:19.327][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:19.327][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:19.328][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:19.328][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:19.328][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:19.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:19.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:19.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:19.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:19.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:19.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:19.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:19.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-24 19:17:19.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:19.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:19.337][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-24 19:17:19.667][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-24 19:17:19.997][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:19.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-24 19:17:20.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-24 19:17:20.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-24 19:17:20.001][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:20.001][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:20.002][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:20.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:20.006][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.009][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:20.009][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:20.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:20.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:20.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.011][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:20.011][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:20.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:20.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:20.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.017][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:20.017][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:20.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:20.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:20.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.020][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.020][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.022][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:20.022][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:20.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.023][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.023][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:20.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.024][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.024][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:20.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.026][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.028][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:20.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:20.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.028][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:20.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.030][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:20.030][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:20.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.031][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:20.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:20.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:20.033][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:20.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.033][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:20.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:20.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:20.044][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-24 19:17:20.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:20.055][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:20.056][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:20.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:20.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:20.057][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 19:17:20.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:20.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:20.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:20.065][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-24 19:17:20.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:20.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-24 19:17:20.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:20.067][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:20.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:20.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:20.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:20.068][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:20.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:20.071][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-24 19:17:20.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:20.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:20.072][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-24 19:17:20.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-24 19:17:20.731][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:20.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-24 19:17:20.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-24 19:17:20.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-24 19:17:20.734][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:20.734][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:20.735][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:20.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:20.743][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.743][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.744][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:20.745][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:20.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.746][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:20.746][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:20.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:20.748][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:20.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.748][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.749][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:20.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.749][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.749][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:20.750][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:20.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.750][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.750][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:20.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.751][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.752][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:20.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.753][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:20.753][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:20.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.753][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:20.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:20.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.755][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:20.755][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:20.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.756][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:20.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.757][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:20.757][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:20.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.758][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:20.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:20.768][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-24 19:17:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:20.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:20.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:20.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:20.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:20.779][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-24 19:17:20.780][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:20.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-24 19:17:20.781][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:20.781][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:20.781][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:20.781][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:20.782][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:20.782][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:20.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:20.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:20.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:20.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:20.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:20.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:20.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:20.786][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-24 19:17:20.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:20.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:20.787][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-24 19:17:21.117][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-24 19:17:21.447][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-06-24 19:17:21.448][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-24 19:17:21.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-24 19:17:21.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-24 19:17:21.450][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-24 19:17:21.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:21.451][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:21.451][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:21.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:21.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:21.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:21.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:21.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:21.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:21.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:21.455][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.455][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.457][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:21.457][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:21.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.458][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.458][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:21.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:21.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.459][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:21.459][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:21.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.459][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.460][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:21.460][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:21.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.460][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.463][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:21.464][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:21.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.464][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.465][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:21.465][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:21.466][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:21.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.466][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.466][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:21.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:21.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.467][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:21.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:21.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:21.469][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:21.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.469][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.469][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:21.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:21.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.470][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:21.471][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:21.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:21.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:21.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:21.480][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-24 19:17:21.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:21.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:21.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:21.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:21.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:21.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:21.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:21.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:21.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:21.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:21.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:21.487][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-24 19:17:21.488][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:21.488][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-24 19:17:21.497][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:21.498][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:21.498][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:21.498][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:21.498][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:21.499][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:21.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:21.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:21.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:21.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:21.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:21.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:21.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:21.502][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-24 19:17:21.503][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:21.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:21.504][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-24 19:17:21.836][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-24 19:17:22.167][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-06-24 19:17:22.168][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-24 19:17:22.168][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-24 19:17:22.169][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-24 19:17:22.170][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-24 19:17:22.170][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:22.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:22.171][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:22.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:22.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:22.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:22.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:22.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:22.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:22.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:22.175][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.175][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.175][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.176][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:22.177][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:22.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.177][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:22.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:22.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.178][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.178][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:22.179][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:22.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:22.180][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:22.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.180][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:22.181][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:22.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.181][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.181][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:22.182][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.182][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:22.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:22.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.183][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:22.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:22.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:22.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:22.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.185][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:22.185][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:22.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.186][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.186][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:22.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:22.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:22.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:22.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.188][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:22.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:22.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:22.200][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-24 19:17:22.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:22.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:22.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:22.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:22.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:22.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:22.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:22.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:22.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:22.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:22.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:22.207][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-24 19:17:22.208][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:22.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-24 19:17:22.208][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:22.208][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:22.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:22.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:22.209][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:22.209][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:22.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:22.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:22.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:22.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:22.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:22.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:22.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:22.213][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-24 19:17:22.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:22.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:22.214][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-24 19:17:22.548][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-24 19:17:23.125][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:23.126][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-24 19:17:23.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-24 19:17:23.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-24 19:17:23.128][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:23.128][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:23.128][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:23.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:23.135][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.137][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:23.137][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:23.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.138][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.138][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:23.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:23.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.139][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:23.139][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:23.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.139][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:23.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:23.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.141][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:23.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:23.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:23.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:23.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.143][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.143][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.144][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.145][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.145][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.146][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:23.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.147][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:23.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.148][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.149][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.150][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:23.150][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:23.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.151][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:23.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:23.152][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:23.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.153][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:23.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.154][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:23.154][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:23.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:23.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:23.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:23.166][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-24 19:17:23.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:23.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:23.172][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-24 19:17:23.172][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:23.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-24 19:17:23.173][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:23.173][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:23.173][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:23.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:23.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:23.174][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:23.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:23.177][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-24 19:17:23.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:23.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:23.178][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-24 19:17:23.509][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-24 19:17:23.842][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:23.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-24 19:17:23.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-24 19:17:23.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-24 19:17:23.844][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:23.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:23.845][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:23.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:23.849][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.849][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.852][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.853][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:23.854][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:23.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.854][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.854][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:23.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:23.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.855][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:23.856][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:23.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:23.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:23.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:23.858][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:23.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:23.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.859][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.859][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:23.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.861][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.861][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.862][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.862][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.863][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:23.863][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.864][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:23.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.865][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.865][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:23.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.867][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:23.867][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:23.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:23.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:23.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.868][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:23.869][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:23.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:23.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.870][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:23.870][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:23.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.871][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.871][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:23.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:23.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:23.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:23.883][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-24 19:17:23.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:23.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:23.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:23.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:23.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:23.888][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-24 19:17:23.888][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:23.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-24 19:17:23.889][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:23.889][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:23.890][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:23.890][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:23.890][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:23.890][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:23.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:23.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:23.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:23.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:23.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:23.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:23.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:23.894][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-24 19:17:23.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:23.895][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:23.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-24 19:17:24.232][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-24 19:17:24.561][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:24.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-24 19:17:24.563][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-24 19:17:24.563][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-24 19:17:24.564][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:24.564][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:24.564][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:24.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:24.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:24.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:24.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:24.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:24.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:24.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:24.568][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.570][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:24.570][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:24.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:24.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:24.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.574][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:24.575][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:24.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.575][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:24.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.576][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:24.577][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:24.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:24.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:24.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.578][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:24.578][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:24.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.579][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:24.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:24.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.580][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:24.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:24.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.581][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:24.581][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.582][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.582][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:24.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:24.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:24.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.584][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:24.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:24.585][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:24.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:24.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:24.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.587][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:24.587][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:24.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.587][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.587][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:24.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:24.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.588][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:24.589][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:24.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.589][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:24.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:24.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:24.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:24.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:24.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:24.600][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-24 19:17:24.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:24.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:24.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:24.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:24.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:24.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:24.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:24.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:24.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:24.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:24.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:24.606][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-24 19:17:24.606][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:24.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-24 19:17:24.607][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:24.607][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:24.607][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:24.608][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:24.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:24.608][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:24.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:24.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:24.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:24.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:24.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:24.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:24.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:24.611][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-24 19:17:24.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:24.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:24.613][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-24 19:17:24.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-24 19:17:25.274][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:25.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-24 19:17:25.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-24 19:17:25.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-24 19:17:25.277][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:25.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:25.278][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:25.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:25.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:25.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:25.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:25.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:25.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:25.281][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[2024-06-24 19:17:25.282][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.283][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.284][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:25.284][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:25.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.285][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:25.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:25.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.286][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:25.286][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:25.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:25.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:25.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.288][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:25.288][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:25.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:25.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:25.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.290][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:25.292][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:25.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.294][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:25.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:25.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.295][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:25.296][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:25.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.296][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:25.297][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.297][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.298][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:25.299][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:25.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.299][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:25.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.300][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:25.301][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:25.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:25.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:25.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.302][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:25.303][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:25.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.304][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:25.305][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:25.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.305][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:25.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:25.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:25.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:25.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:25.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:25.315][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-24 19:17:25.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:25.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:25.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:25.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:25.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:25.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:25.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:25.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:25.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:25.323][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-24 19:17:25.323][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:25.324][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-24 19:17:25.324][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:25.324][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:25.324][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:25.325][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:25.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:25.325][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:25.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:25.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:25.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:25.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:25.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:25.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:25.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:25.329][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-24 19:17:25.329][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:25.329][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:25.330][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-24 19:17:25.673][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-24 19:17:26.000][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:26.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-24 19:17:26.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-24 19:17:26.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-24 19:17:26.003][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:26.003][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:26.004][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:26.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.007][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.TRACE[2024-06-24 19:17:26.007][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.007][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.009][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:26.009][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:26.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:26.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:26.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.011][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:26.011][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:26.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:26.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:26.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.013][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:26.013][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:26.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:26.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:26.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.015][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.016][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:26.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:26.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.017][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:26.018][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.018][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:26.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.022][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.022][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.023][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.024][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:26.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:26.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.025][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:26.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:26.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.026][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:26.026][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:26.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.027][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.027][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:26.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.028][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:26.028][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:26.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.029][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:26.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:26.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:26.038][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-24 19:17:26.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:26.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:26.044][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-24 19:17:26.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:26.044][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-24 19:17:26.045][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:26.045][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:26.045][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:26.045][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:26.046][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:26.046][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:26.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:26.051][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-24 19:17:26.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:26.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:26.052][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-24 19:17:26.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-24 19:17:26.719][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:26.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-24 19:17:26.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-24 19:17:26.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-24 19:17:26.721][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:26.722][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:26.722][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:26.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:26.725][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.726][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.727][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:26.728][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:26.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.728][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.728][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:26.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:26.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.729][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:26.729][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:26.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:26.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:26.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.731][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:26.731][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:26.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:26.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:26.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.733][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.733][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.734][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:26.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.735][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:26.735][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:26.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.736][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:26.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.736][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:26.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.737][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.738][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.738][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:26.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.739][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:26.739][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:26.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:26.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:26.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.744][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:26.744][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:26.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.745][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.745][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:26.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:26.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.746][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:26.746][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:26.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:26.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:26.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:26.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:26.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:26.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:26.757][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-24 19:17:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:26.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:26.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:26.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:26.762][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-24 19:17:26.762][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:26.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-24 19:17:26.763][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:26.763][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:26.764][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:26.764][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:26.764][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:26.764][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:26.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:26.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:26.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:26.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:26.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:26.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:26.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:26.768][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-24 19:17:26.768][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:26.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:26.770][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-24 19:17:27.102][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-24 19:17:27.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:27.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-24 19:17:27.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-24 19:17:27.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-24 19:17:27.433][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:27.433][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:27.433][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:27.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:27.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:27.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:27.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:27.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:27.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:27.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:27.438][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.440][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:27.440][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:27.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.441][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:27.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:27.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.442][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:27.442][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:27.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.443][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:27.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.444][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:27.445][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:27.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.445][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.445][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:27.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:27.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:27.447][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:27.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.447][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:27.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:27.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:27.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:27.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.449][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.449][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:27.450][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.450][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.450][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:27.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.451][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:27.452][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:27.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.452][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:27.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:27.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.453][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:27.453][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:27.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:27.455][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:27.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.456][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:27.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:27.457][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:27.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.458][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.461][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:27.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:27.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:27.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:27.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:27.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:27.473][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-24 19:17:27.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:27.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:27.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:27.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:27.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:27.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:27.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:27.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:27.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:27.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:27.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:27.479][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-24 19:17:27.479][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:27.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-24 19:17:27.480][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:27.480][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:27.481][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:27.481][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:27.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:27.481][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:27.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:27.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:27.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:27.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:27.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:27.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:27.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:27.485][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-24 19:17:27.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:27.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:27.486][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-24 19:17:27.815][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-24 19:17:28.147][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:28.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-24 19:17:28.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-24 19:17:28.150][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-24 19:17:28.150][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:28.151][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:28.151][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:28.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:28.159][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.160][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.160][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.162][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:28.162][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:28.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.163][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:28.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:28.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.164][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:28.164][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:28.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:28.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:28.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.166][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:28.167][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:28.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.167][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.167][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:28.168][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:28.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.168][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:28.169][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:28.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.169][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:28.170][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.171][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:28.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.172][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.172][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.174][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:28.174][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:28.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.174][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:28.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:28.176][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:28.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.177][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:28.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:28.178][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:28.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:28.192][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-24 19:17:28.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:28.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:28.199][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-24 19:17:28.200][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:28.200][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-24 19:17:28.201][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:28.201][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:28.201][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:28.201][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:28.202][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:28.202][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:28.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:28.206][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-24 19:17:28.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:28.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:28.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-24 19:17:28.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-24 19:17:28.868][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:28.869][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-24 19:17:28.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-24 19:17:28.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-24 19:17:28.872][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:28.872][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:28.872][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:28.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:28.877][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.877][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.878][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.879][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:28.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:28.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.880][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.880][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:28.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.885][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:28.885][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:28.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.886][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:28.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:28.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:28.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.888][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:28.889][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:28.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.890][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:28.890][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:28.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.890][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.891][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:28.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:28.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.893][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.894][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.895][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:28.896][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:28.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.896][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:28.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:28.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.898][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:28.898][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:28.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.898][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.899][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:28.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:28.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:28.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.901][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:28.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:28.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:28.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:28.911][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-24 19:17:28.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:28.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:28.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:28.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:28.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:28.922][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-24 19:17:28.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:28.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-24 19:17:28.923][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:28.923][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:28.923][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:28.924][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:28.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:28.924][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:28.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:28.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:28.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:28.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:28.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:28.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:28.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:28.929][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-24 19:17:28.930][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:28.930][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:28.931][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-24 19:17:29.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-24 19:17:29.592][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:29.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-24 19:17:29.594][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-24 19:17:29.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-24 19:17:29.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:29.595][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:29.596][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:29.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:29.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:29.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:29.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:29.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:29.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:29.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:29.600][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.600][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.601][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.602][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:29.602][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:29.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.603][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:29.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.604][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:29.604][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:29.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.605][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:29.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:29.606][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:29.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.607][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:29.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.608][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:29.608][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:29.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.609][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.613][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:29.614][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:29.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.614][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.615][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:29.615][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.616][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:29.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:29.617][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:29.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.618][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.619][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:29.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:29.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.620][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:29.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.621][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:29.621][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:29.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.622][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:29.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:29.623][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:29.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.624][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:29.634][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-24 19:17:29.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:29.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:29.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:29.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:29.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:29.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:29.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:29.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:29.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:29.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:29.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:29.642][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-24 19:17:29.643][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:29.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-24 19:17:29.644][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:29.644][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:29.644][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:29.644][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:29.645][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:29.645][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:29.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:29.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:29.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:29.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:29.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:29.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:29.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:29.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-24 19:17:29.649][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:29.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:29.650][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-24 19:17:29.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-24 19:17:30.312][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:30.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-24 19:17:30.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-24 19:17:30.315][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-24 19:17:30.316][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:30.316][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:30.316][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:30.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:30.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:30.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:30.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:30.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:30.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:30.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:30.320][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.321][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.322][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:30.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:30.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.323][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:30.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:30.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.324][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:30.324][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:30.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.324][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.325][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:30.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:30.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.326][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:30.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:30.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:30.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:30.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.327][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:30.328][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:30.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.328][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:30.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:30.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.329][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:30.329][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:30.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.330][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:30.330][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.331][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:30.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.335][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:30.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:30.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.337][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:30.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:30.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:30.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:30.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.339][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.340][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:30.340][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:30.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.341][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.341][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:30.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:30.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.342][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:30.342][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:30.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.342][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.343][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:30.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:30.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:30.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:30.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:30.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:30.352][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-24 19:17:30.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:30.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:30.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:30.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:30.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:30.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:30.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:30.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:30.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:30.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:30.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:30.358][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-24 19:17:30.358][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:30.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-24 19:17:30.359][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:30.359][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:30.359][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:30.359][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:30.359][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:30.360][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:30.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:30.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:30.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:30.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:30.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:30.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:30.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:30.365][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-24 19:17:30.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:30.366][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:30.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-24 19:17:30.695][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-24 19:17:31.041][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:31.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-24 19:17:31.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-24 19:17:31.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-24 19:17:31.044][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:31.044][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:31.044][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:31.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:31.048][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.050][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:31.050][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:31.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:31.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:31.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.052][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:31.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:31.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.052][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:31.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.054][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:31.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:31.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.054][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:31.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.056][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.056][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:31.058][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:31.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.058][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:31.058][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:31.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.060][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.060][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.061][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.062][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:31.062][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:31.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:31.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:31.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.065][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:31.067][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:31.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.067][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:31.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.068][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:31.069][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:31.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.069][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:31.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:31.079][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-24 19:17:31.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:31.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:31.084][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-24 19:17:31.085][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:31.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-24 19:17:31.085][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:31.086][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:31.086][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:31.086][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:31.086][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:31.087][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:31.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:31.090][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-24 19:17:31.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:31.091][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:31.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-24 19:17:31.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-24 19:17:31.754][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:31.755][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-24 19:17:31.756][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-24 19:17:31.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-24 19:17:31.757][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:31.757][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:31.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:31.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.761][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.TRACE[2024-06-24 19:17:31.761][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.763][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:31.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:31.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.764][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.764][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:31.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:31.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.765][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:31.766][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:31.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.766][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:31.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:31.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.767][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:31.767][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:31.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.768][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:31.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:31.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.769][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.770][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:31.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.771][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:31.771][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:31.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.772][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.772][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:31.772][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.773][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.773][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:31.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.774][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.776][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:31.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:31.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:31.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:31.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.777][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:31.778][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:31.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.778][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:31.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:31.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.779][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:31.780][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:31.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:31.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:31.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:31.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:31.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:31.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:31.792][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-24 19:17:31.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:31.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:31.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:31.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:31.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:31.798][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-24 19:17:31.798][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:31.799][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-24 19:17:31.799][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:31.799][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:31.799][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:31.800][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:31.800][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:31.800][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:31.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:31.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:31.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:31.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:31.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:31.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:31.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:31.804][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-24 19:17:31.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:31.805][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:31.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-24 19:17:32.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-24 19:17:32.465][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:32.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-24 19:17:32.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-24 19:17:32.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-24 19:17:32.467][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:32.468][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:32.468][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:32.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:32.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:32.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:32.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:32.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:32.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:32.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:32.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.475][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.477][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:32.477][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:32.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.477][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.478][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:32.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:32.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.479][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:32.479][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:32.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.479][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:32.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:32.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:32.481][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:32.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:32.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:32.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.482][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:32.483][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:32.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.483][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:32.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:32.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.484][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:32.484][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:32.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.485][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.485][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:32.485][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.486][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:32.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.487][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:32.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:32.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:32.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:32.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.489][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:32.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:32.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:32.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:32.491][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:32.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.491][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.492][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:32.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:32.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.492][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:32.493][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:32.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.493][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.493][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:32.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:32.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:32.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:32.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:32.505][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-24 19:17:32.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:32.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:32.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:32.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:32.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:32.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:32.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:32.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:32.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:32.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:32.510][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-24 19:17:32.511][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:32.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-24 19:17:32.511][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:32.512][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:32.512][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:32.512][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:32.512][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:32.512][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:32.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:32.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:32.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:32.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:32.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:32.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:32.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:32.516][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-24 19:17:32.516][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:32.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:32.517][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-24 19:17:32.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-24 19:17:33.180][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:33.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-24 19:17:33.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-24 19:17:33.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-24 19:17:33.183][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:33.183][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:33.183][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:33.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:33.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:33.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:33.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:33.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:33.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:33.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:33.187][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.188][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.192][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:33.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:33.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.193][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:33.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.194][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:33.195][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:33.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.195][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:33.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:33.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:33.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.197][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.198][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.198][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.199][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.200][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:33.200][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.201][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:33.201][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:33.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.203][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.203][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.205][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:33.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:33.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.205][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:33.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:33.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.207][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:33.207][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:33.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.207][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.207][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:33.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:33.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:33.209][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:33.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.209][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:33.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:33.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:33.221][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-24 19:17:33.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:33.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:33.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:33.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:33.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:33.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:33.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:33.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:33.226][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-24 19:17:33.227][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:33.227][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-24 19:17:33.227][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:33.228][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:33.228][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:33.228][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:33.228][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:33.229][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:33.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:33.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:33.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:33.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:33.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:33.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:33.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:33.232][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-24 19:17:33.233][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:33.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:33.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-24 19:17:33.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-24 19:17:33.892][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:33.893][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-24 19:17:33.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-24 19:17:33.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-24 19:17:33.895][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:33.895][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:33.896][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:33.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:33.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:33.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:33.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:33.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:33.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:33.898][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[2024-06-24 19:17:33.899][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.899][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.901][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:33.901][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:33.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.902][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.902][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:33.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:33.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.903][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:33.903][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:33.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.903][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.908][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:33.908][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:33.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:33.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.910][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:33.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.911][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:33.912][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:33.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.912][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:33.913][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.913][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.914][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.914][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.916][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:33.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:33.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.917][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:33.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.918][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:33.918][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:33.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.919][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:33.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:33.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.919][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:33.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:33.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.920][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.920][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:33.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:33.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:33.930][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-24 19:17:33.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:33.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:33.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:33.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:33.940][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:33.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:33.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:33.942][private$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[2024-06-24 19:17:34.407][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[2024-06-24 19:17:34.871][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:34.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-24 19:17:34.873][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-24 19:17:34.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.883][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.TRACE[2024-06-24 19:17:34.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.890][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.TRACE[2024-06-24 19:17:34.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.939][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.TRACE[2024-06-24 19:17:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.949][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[2024-06-24 19:17:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.954][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.TRACE[2024-06-24 19:17:34.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.967][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.TRACE[2024-06-24 19:17:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.977][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[2024-06-24 19:17:34.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.982][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.TRACE[2024-06-24 19:17:34.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:34.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:34.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:34.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:34.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:34.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:34.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:34.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:34.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:34.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:35.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:35.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:35.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:35.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:35.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:35.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:35.004][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[2024-06-24 19:17:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:35.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:35.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:35.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:35.023][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[2024-06-24 19:17:35.024][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:35.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:35.025][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:35.355][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:35.684][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:35.685][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-24 19:17:35.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-24 19:17:35.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:35.688][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:35.688][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:35.689][private$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[2024-06-24 19:17:36.027][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[2024-06-24 19:17:36.356][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:36.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-24 19:17:36.358][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-24 19:17:36.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:36.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:36.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:36.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:36.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:36.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:36.362][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[2024-06-24 19:17:36.362][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-24 19:17:36.362][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:36.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-24 19:17:36.363][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:36.363][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:36.364][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:36.364][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:36.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:36.364][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:36.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:36.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:36.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:36.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:36.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:36.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:36.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:36.368][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-24 19:17:36.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:36.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:36.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-24 19:17:36.707][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-24 19:17:37.056][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:37.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-24 19:17:37.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-24 19:17:37.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-24 19:17:37.059][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:37.059][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:37.059][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:37.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.063][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.065][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:37.066][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:37.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.066][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:37.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:37.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.067][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:37.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:37.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.068][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:37.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:37.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.069][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:37.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:37.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.070][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:37.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:37.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.071][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.073][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.073][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.074][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.075][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:37.075][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:37.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.076][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:37.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:37.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.077][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.078][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:37.078][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:37.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.079][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:37.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:37.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.080][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:37.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:37.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.081][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:37.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:37.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:37.085][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:37.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.086][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.086][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:37.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:37.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.096][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-24 19:17:37.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.101][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.TRACE[2024-06-24 19:17:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:37.107][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-24 19:17:37.107][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:37.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-24 19:17:37.108][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:37.108][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:37.108][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:37.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:37.109][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:37.109][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:37.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.114][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.DEBUG[2024-06-24 19:17:37.114][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-24 19:17:37.115][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:37.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:37.116][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-24 19:17:37.445][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-24 19:17:37.778][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:37.779][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-24 19:17:37.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-24 19:17:37.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-24 19:17:37.781][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:37.781][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:37.781][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:37.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.785][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.785][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.787][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:37.787][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:37.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:37.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:37.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.789][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:37.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:37.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.790][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:37.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:37.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.791][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:37.791][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:37.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:37.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:37.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.793][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.793][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.793][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:37.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.794][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.795][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:37.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.795][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.795][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:37.796][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:37.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.796][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.796][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:37.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:37.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.797][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.799][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:37.799][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:37.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.802][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:37.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:37.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.804][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:37.804][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:37.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.805][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:37.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:37.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.806][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:37.806][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:37.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.807][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:37.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:37.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:37.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.817][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-24 19:17:37.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.825][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[2024-06-24 19:17:37.825][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:37.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:37.826][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:37.827][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 19:17:37.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.915][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[2024-06-24 19:17:37.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.941][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[2024-06-24 19:17:37.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.964][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[2024-06-24 19:17:37.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.976][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.TRACE[2024-06-24 19:17:37.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:37.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:37.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:37.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:37.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:37.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:37.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:37.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:37.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:37.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:37.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:37.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:38.010][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:38.010][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 19:17:38.010][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:38.011][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 19:17:38.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.014][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[2024-06-24 19:17:38.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.026][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[2024-06-24 19:17:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.033][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[2024-06-24 19:17:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.040][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[2024-06-24 19:17:38.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.045][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[2024-06-24 19:17:38.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.060][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.TRACE[2024-06-24 19:17:38.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.070][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.TRACE[2024-06-24 19:17:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.087][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[2024-06-24 19:17:38.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.102][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.TRACE[2024-06-24 19:17:38.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:38.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.124][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:38.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:38.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:38.127][biodb::testThat]
biodb.INFO [2024-06-24 19:17:38.127][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-24 19:17:38.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:38.128][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:38.129][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 19:17:38.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 19:17:38.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:38.137][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[2024-06-24 19:17:38.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:38.138][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:38.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:38.468][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:38.811][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:38.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-24 19:17:38.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-24 19:17:38.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:38.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:38.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:38.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:38.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:38.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:38.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:38.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:38.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:38.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:38.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:38.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:38.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:38.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:38.821][private$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[2024-06-24 19:17:39.153][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[2024-06-24 19:17:39.488][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:39.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-24 19:17:39.489][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-24 19:17:39.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:39.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:39.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:39.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:39.501][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:39.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:39.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.506][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.508][private$selectFields]
biodb.TRACE[2024-06-24 19:17:39.510][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:39.511][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:39.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.511][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.512][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.513][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.514][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.514][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:39.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.519][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 19:17:39.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:39.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.524][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.524][private$selectFields]
biodb.TRACE[2024-06-24 19:17:39.524][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:39.525][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:39.525][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.525][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.527][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.527][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.527][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.528][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.528][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:39.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.531][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:39.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:39.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.535][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.536][private$selectFields]
biodb.TRACE[2024-06-24 19:17:39.536][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:39.536][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:39.536][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.537][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.537][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.538][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.539][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:39.539][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.539][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.539][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.540][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.543][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 19:17:39.543][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:39.543][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:39.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:39.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:39.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:39.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:39.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:39.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:39.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:39.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:39.566][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[2024-06-24 19:17:39.567][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[2024-06-24 19:17:39.568][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:39.568][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:39.569][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:39.899][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:40.228][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:40.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-24 19:17:40.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-24 19:17:40.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:40.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:40.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:40.232][private$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[2024-06-24 19:17:40.562][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[2024-06-24 19:17:40.893][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:40.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-24 19:17:40.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-24 19:17:40.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.899][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.TRACE[2024-06-24 19:17:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:40.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.904][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[2024-06-24 19:17:40.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:40.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.913][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.TRACE[2024-06-24 19:17:40.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:40.922][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:40.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:40.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.933][private$selectFields]
biodb.TRACE[2024-06-24 19:17:40.933][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:40.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:40.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.934][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.934][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.935][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.935][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.935][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.936][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.936][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.937][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:40.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.940][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 19:17:40.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:40.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.953][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.953][private$selectFields]
biodb.TRACE[2024-06-24 19:17:40.954][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:40.954][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:40.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.954][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.955][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.955][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.956][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.959][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.959][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.960][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:40.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.963][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:40.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.968][private$selectFields]
biodb.TRACE[2024-06-24 19:17:40.968][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:40.968][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:40.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.969][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.970][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.970][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:40.971][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.971][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.971][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:40.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.974][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 19:17:40.975][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:40.975][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:40.977][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:40.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:40.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:40.979][biodb::testThat]
biodb.INFO [2024-06-24 19:17:40.979][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-24 19:17:40.979][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:40.980][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:40.980][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 19:17:40.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 19:17:40.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:40.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:40.988][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[2024-06-24 19:17:40.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:40.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 19:17:40.992][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:40.992][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 19:17:40.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:40.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:40.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:40.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:40.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:40.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:40.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:40.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:40.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:40.998][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[2024-06-24 19:17:40.999][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:40.999][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 19:17:40.999][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.000][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 19:17:41.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.007][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.TRACE[2024-06-24 19:17:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.010][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:41.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.015][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.015][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.015][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.018][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.019][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.019][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.022][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 19:17:41.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.027][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.027][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.027][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.027][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.028][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.029][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.029][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.029][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.030][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.030][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.031][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.033][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:41.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.038][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.038][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.038][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.039][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.039][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.040][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.040][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.040][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.040][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.041][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.041][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.042][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.045][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 19:17:41.045][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:41.045][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:41.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.054][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[2024-06-24 19:17:41.055][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[2024-06-24 19:17:41.056][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 19:17:41.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.056][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 19:17:41.057][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[2024-06-24 19:17:41.058][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 19:17:41.059][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.059][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 19:17:41.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.067][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.TRACE[2024-06-24 19:17:41.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.077][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:41.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.081][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.082][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.082][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.082][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.082][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.084][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.084][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.085][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.085][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.088][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 19:17:41.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.093][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.093][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.093][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.094][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.095][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.095][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.097][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.099][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:41.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.102][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.TRACE[2024-06-24 19:17:41.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.104][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.104][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.104][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.105][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.105][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.106][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.107][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.107][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.107][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.108][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.111][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 19:17:41.111][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:41.111][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:41.113][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:41.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:41.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:41.115][biodb::testThat]
biodb.INFO [2024-06-24 19:17:41.116][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-24 19:17:41.116][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:41.116][biodb::testThat]
biodb.TRACE[2024-06-24 19:17:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 19:17:41.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 19:17:41.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:41.125][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[2024-06-24 19:17:41.126][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 19:17:41.127][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.127][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 19:17:41.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.130][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.TRACE[2024-06-24 19:17:41.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.133][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[2024-06-24 19:17:41.134][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 19:17:41.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.135][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 19:17:41.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.138][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[2024-06-24 19:17:41.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.146][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:41.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.150][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.150][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.151][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.155][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.155][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.155][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.155][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.156][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.159][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 19:17:41.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.164][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.164][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.164][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.165][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.166][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.166][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.166][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.167][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.167][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.167][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:41.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.175][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.175][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.175][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.176][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.176][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.176][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.176][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.177][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.177][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.178][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.178][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.179][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.182][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 19:17:41.182][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:41.182][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:41.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.194][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[2024-06-24 19:17:41.195][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[2024-06-24 19:17:41.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.196][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 19:17:41.196][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.197][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 19:17:41.197][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[2024-06-24 19:17:41.198][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:41.199][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 19:17:41.199][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:41.199][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 19:17:41.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.207][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[2024-06-24 19:17:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.215][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 19:17:41.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.220][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.220][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.220][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.221][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.221][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.223][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.223][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.223][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.224][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.227][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 19:17:41.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.231][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.232][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.234][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.235][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.236][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.237][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.237][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 19:17:41.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.243][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[2024-06-24 19:17:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.245][private$selectFields]
biodb.TRACE[2024-06-24 19:17:41.245][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 19:17:41.245][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 19:17:41.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.246][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.247][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.247][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.248][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 19:17:41.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.249][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 19:17:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.252][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 19:17:41.252][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 19:17:41.252][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 19:17:41.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 19:17:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:41.259][biodb::testThat]
biodb.INFO [2024-06-24 19:17:41.259][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-06-24 19:17:41.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:41.260][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:41.260][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-24 19:17:41.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:41.261][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-24 19:17:41.261][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:41.261][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:41.261][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:41.262][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:41.262][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:41.262][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:41.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:41.265][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-24 19:17:41.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:41.266][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:41.267][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-24 19:17:41.596][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-24 19:17:41.929][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:41.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-24 19:17:41.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-24 19:17:41.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-24 19:17:41.932][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:41.933][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:41.933][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:41.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:41.937][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.937][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.937][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.939][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:41.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:41.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.939][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.940][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:41.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:41.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:41.941][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:41.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.941][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.942][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:41.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.942][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.942][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:41.943][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:41.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.943][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.943][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:41.944][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:41.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.944][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.944][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.945][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:41.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.945][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:41.945][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:41.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.946][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:41.946][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:41.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.947][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:41.947][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:41.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:41.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:41.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:41.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:41.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:41.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:41.957][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-24 19:17:41.957][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-24 19:17:41.959][biodb::testThat]
biodb.INFO [2024-06-24 19:17:41.960][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-24 19:17:41.960][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:41.960][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:41.963][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-24 19:17:41.963][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-24 19:17:41.964][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-24 19:17:41.964][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-24 19:17:41.964][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-24 19:17:41.965][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:41.965][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:41.965][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:41.965][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:41.965][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:41.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:41.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:41.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:41.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:41.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:41.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:41.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:41.969][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-24 19:17:41.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:41.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:41.970][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-24 19:17:42.302][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-24 19:17:42.631][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:42.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-24 19:17:42.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-24 19:17:42.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:42.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:42.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:42.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:42.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:42.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:42.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:42.637][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-24 19:17:42.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:42.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:42.638][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-24 19:17:42.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-06-24 19:17:43.304][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:43.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-24 19:17:43.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-24 19:17:43.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:43.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:43.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:43.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:43.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:43.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:43.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:43.313][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-24 19:17:43.314][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:43.314][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:43.314][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-24 19:17:43.645][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-24 19:17:43.975][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:43.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-24 19:17:43.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-24 19:17:43.977][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-24 19:17:43.978][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:43.978][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-24 19:17:43.978][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:43.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:43.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:43.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:43.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:43.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:43.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:43.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:43.982][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.982][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.983][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.984][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:43.984][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:43.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.985][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:43.985][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:43.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.986][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:43.986][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:43.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.987][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:43.987][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:43.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.988][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:43.988][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:43.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.989][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:43.989][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:43.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.989][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:43.990][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:43.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.990][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:43.991][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:43.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.991][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:43.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:43.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.992][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.992][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:43.992][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:43.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:43.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:43.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:43.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:43.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:43.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:43.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:44.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:44.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:44.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:44.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:44.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.002][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.TRACE[2024-06-24 19:17:44.003][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.003][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.004][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:44.005][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:44.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.005][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.005][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:44.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:44.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.006][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:44.007][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:44.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.007][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:44.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.008][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:44.008][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:44.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:44.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:44.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.010][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.011][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.012][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.012][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.013][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.014][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:44.014][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:44.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.014][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.015][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:44.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:44.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.015][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.016][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.016][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.017][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:44.017][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:44.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:44.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:44.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.019][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:44.019][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:44.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.020][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.020][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:44.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:44.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:44.021][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:44.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.021][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:44.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:44.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:44.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:44.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:44.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:44.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:44.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:44.032][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.032][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.032][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.034][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:44.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:44.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.035][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:44.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:44.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.035][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:44.036][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:44.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.036][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:44.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.037][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:44.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:44.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.038][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:44.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:44.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.039][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.039][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.040][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:44.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.041][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.041][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:44.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.043][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:44.043][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:44.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.043][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:44.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:44.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.045][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.045][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.045][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.046][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:44.047][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:44.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.047][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:44.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.048][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:44.048][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:44.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.052][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:44.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:44.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.053][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:44.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:44.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:44.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:44.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:44.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:44.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:44.068][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-24 19:17:44.069][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-24 19:17:44.069][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-24 19:17:44.072][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.073][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-06-24 19:17:44.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:44.073][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.079][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.080][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-06-24 19:17:44.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:44.080][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.082][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.083][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-06-24 19:17:44.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:44.083][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:44.084][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[2024-06-24 19:17:44.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:44.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:44.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:44.491][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:44.957][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:44.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-24 19:17:44.959][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-24 19:17:44.962][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:44.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:44.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:44.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:44.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:44.964][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 19:17:44.964][biodb::testThat]
biodb.INFO [2024-06-24 19:17:44.965][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-24 19:17:44.965][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:44.965][biodb::testThat]
biodb.ERROR[2024-06-24 19:17:44.969][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-24 19:17:44.973][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-24 19:17:44.977][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 19:17:44.977][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 19:17:44.977][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 19:17:44.977][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 19:17:44.978][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:44.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:44.978][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:44.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:44.978][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 19:17:44.981][biodb::testContext]
biodb.INFO [2024-06-24 19:17:44.982][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:44.982][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-24 19:17:44.982][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:44.982][biodb::testContext]
biodb.INFO [2024-06-24 19:17:44.983][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:44.983][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:44.985][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:44.985][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 19:17:44.985][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.986][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[2024-06-24 19:17:44.986][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 19:17:44.986][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.987][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 19:17:44.987][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.988][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 19:17:44.988][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 19:17:44.988][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 19:17:44.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.989][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 19:17:44.989][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 19:17:44.990][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.990][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 19:17:44.991][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 19:17:44.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.991][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 19:17:44.992][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 19:17:44.992][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 19:17:44.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.993][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 19:17:44.993][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.994][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 19:17:44.994][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 19:17:44.994][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 19:17:44.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.995][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:44.995][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 19:17:44.995][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 19:17:44.996][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 19:17:44.996][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 19:17:44.996][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 19:17:44.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.997][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 19:17:44.997][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 19:17:44.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.998][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 19:17:44.998][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 19:17:44.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:44.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:44.999][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 19:17:44.999][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 19:17:44.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:44.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.000][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 19:17:45.000][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 19:17:45.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.001][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 19:17:45.001][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 19:17:45.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.002][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[2024-06-24 19:17:45.002][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:45.002][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 19:17:45.007][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 19:17:45.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.008][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 19:17:45.008][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 19:17:45.008][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 19:17:45.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.009][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[2024-06-24 19:17:45.009][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 19:17:45.013][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.013][self$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[2024-06-24 19:17:45.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:45.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.014][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.014][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:45.015][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:45.015][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.015][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 19:17:45.015][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:45.015][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:45.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:45.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.017][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.018][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:45.018][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:45.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.018][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.019][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 19:17:45.019][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.019][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:45.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.020][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:45.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.020][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.020][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.021][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:45.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:45.021][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.021][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:45.022][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:45.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:45.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.024][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.024][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:45.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:45.024][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.025][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.025][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 19:17:45.025][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.026][self$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[2024-06-24 19:17:45.026][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.026][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:45.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.026][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.027][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.027][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.027][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:45.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:45.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.028][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 19:17:45.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:45.028][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.029][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:45.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:45.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.030][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.030][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:45.031][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:45.031][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.031][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.031][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 19:17:45.032][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.032][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:45.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.032][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:45.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.033][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.033][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:45.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:45.034][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.034][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 19:17:45.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:45.035][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.035][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.035][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:45.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.036][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:45.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.037][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.037][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:45.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:45.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.038][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:45.038][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:45.038][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.039][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[2024-06-24 19:17:45.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.042][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[2024-06-24 19:17:45.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.043][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[2024-06-24 19:17:45.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.044][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[2024-06-24 19:17:45.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.046][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[2024-06-24 19:17:45.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.054][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[2024-06-24 19:17:45.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.055][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[2024-06-24 19:17:45.055][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 19:17:45.056][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 19:17:45.056][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 19:17:45.056][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 19:17:45.057][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:45.057][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 19:17:45.057][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:45.057][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:45.058][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 19:17:45.058][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 19:17:45.058][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:45.059][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 19:17:45.059][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:45.059][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:45.060][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 19:17:45.060][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 19:17:45.060][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 19:17:45.061][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 19:17:45.061][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:45.061][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 19:17:45.062][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 19:17:45.062][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 19:17:45.062][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 19:17:45.063][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 19:17:45.063][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 19:17:45.063][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 19:17:45.064][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 19:17:45.064][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 19:17:45.064][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 19:17:45.064][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 19:17:45.065][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 19:17:45.065][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 19:17:45.065][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 19:17:45.066][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 19:17:45.066][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 19:17:45.066][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 19:17:45.067][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 19:17:45.067][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 19:17:45.067][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 19:17:45.068][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 19:17:45.068][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 19:17:45.068][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 19:17:45.069][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 19:17:45.069][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 19:17:45.069][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 19:17:45.070][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 19:17:45.070][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 19:17:45.070][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 19:17:45.071][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 19:17:45.071][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 19:17:45.071][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 19:17:45.072][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 19:17:45.072][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 19:17:45.072][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 19:17:45.072][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 19:17:45.073][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 19:17:45.073][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 19:17:45.073][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 19:17:45.074][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 19:17:45.074][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 19:17:45.074][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 19:17:45.075][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 19:17:45.075][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 19:17:45.075][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 19:17:45.076][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 19:17:45.076][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 19:17:45.076][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:45.077][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:45.077][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 19:17:45.077][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 19:17:45.077][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 19:17:45.078][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 19:17:45.078][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 19:17:45.078][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 19:17:45.079][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 19:17:45.079][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 19:17:45.079][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 19:17:45.080][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 19:17:45.080][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 19:17:45.080][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 19:17:45.081][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 19:17:45.081][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 19:17:45.081][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 19:17:45.082][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 19:17:45.082][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:45.082][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:45.083][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.083][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.091][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[2024-06-24 19:17:45.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.096][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[2024-06-24 19:17:45.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.101][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[2024-06-24 19:17:45.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.102][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[2024-06-24 19:17:45.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.104][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[2024-06-24 19:17:45.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.106][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[2024-06-24 19:17:45.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:45.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:45.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:45.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:45.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:45.108][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:45.109][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 19:17:45.109][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.109][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.110][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:45.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.110][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.111][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 19:17:45.111][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 19:17:45.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:45.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 19:17:45.112][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.113][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:45.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:45.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:45.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:45.114][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:45.114][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 19:17:45.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:45.115][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:45.115][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:45.115][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 19:17:45.115][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 19:17:45.115][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:45.116][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:45.116][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 19:17:45.117][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:45.117][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:45.117][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:45.118][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 19:17:45.118][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 19:17:45.119][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 19:17:45.119][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 19:17:45.119][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:45.120][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:45.120][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 19:17:45.120][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 19:17:45.120][biodb::testThat]
biodb.INFO [2024-06-24 19:17:45.121][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-06-24 19:17:45.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:45.121][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:45.122][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 19:17:45.123][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:45.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:45.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-24 19:17:45.448][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-24 19:17:45.932][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:45.933][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-24 19:17:45.934][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-24 19:17:45.935][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[2024-06-24 19:17:45.936][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:45.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:45.937][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:46.271][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:46.601][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:46.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-24 19:17:46.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-24 19:17:46.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:46.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:46.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:46.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:46.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:46.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:46.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:46.607][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:46.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:46.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:46.609][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:46.938][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:47.268][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:47.269][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-24 19:17:47.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-06-24 19:17:47.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:47.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:47.283][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[2024-06-24 19:17:47.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:47.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 19:17:47.285][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:47.285][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 19:17:47.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.288][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[2024-06-24 19:17:47.289][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[2024-06-24 19:17:47.290][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:47.290][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 19:17:47.290][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:47.291][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 19:17:47.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:47.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:47.298][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[2024-06-24 19:17:47.299][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:47.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 19:17:47.299][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:47.300][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 19:17:47.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:47.303][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[2024-06-24 19:17:47.309][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:47.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 19:17:47.310][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:47.310][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 19:17:47.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.313][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[2024-06-24 19:17:47.314][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[2024-06-24 19:17:47.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:47.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:47.316][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:47.654][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:47.983][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:47.983][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-24 19:17:47.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-24 19:17:47.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:47.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:47.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:47.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:47.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:47.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:47.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 19:17:47.990][biodb::testThat]
biodb.INFO [2024-06-24 19:17:47.990][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-06-24 19:17:47.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:47.991][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:47.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:47.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:47.993][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:47.993][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:48.323][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:48.653][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:48.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-24 19:17:48.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-24 19:17:48.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:48.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:48.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:48.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:48.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:48.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:48.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:48.659][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[2024-06-24 19:17:48.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:48.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:48.661][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:48.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:49.321][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:49.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-24 19:17:49.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-24 19:17:49.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:49.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 19:17:49.328][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 19:17:49.329][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 19:17:49.329][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 19:17:49.329][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 19:17:49.329][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.330][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.330][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 19:17:49.332][biodb::testContext]
biodb.INFO [2024-06-24 19:17:49.332][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:49.332][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-24 19:17:49.333][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:49.333][biodb::testContext]
biodb.INFO [2024-06-24 19:17:49.334][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:49.334][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:49.336][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:49.336][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 19:17:49.336][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.337][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 19:17:49.337][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.338][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 19:17:49.339][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.339][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 19:17:49.340][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 19:17:49.340][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 19:17:49.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.341][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 19:17:49.341][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 19:17:49.341][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.342][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 19:17:49.343][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 19:17:49.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.343][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 19:17:49.344][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 19:17:49.344][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 19:17:49.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 19:17:49.345][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.346][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 19:17:49.346][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 19:17:49.347][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 19:17:49.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.348][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:49.348][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 19:17:49.348][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 19:17:49.348][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 19:17:49.349][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 19:17:49.349][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 19:17:49.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.350][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 19:17:49.350][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 19:17:49.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.351][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 19:17:49.351][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 19:17:49.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.352][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 19:17:49.352][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 19:17:49.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.353][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[2024-06-24 19:17:49.353][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 19:17:49.353][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 19:17:49.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.354][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 19:17:49.355][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 19:17:49.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.356][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:49.356][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 19:17:49.360][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 19:17:49.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.361][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 19:17:49.361][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 19:17:49.362][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 19:17:49.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.362][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[2024-06-24 19:17:49.363][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 19:17:49.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.363][self$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[2024-06-24 19:17:49.364][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.364][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:49.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.364][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.365][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.365][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:49.365][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:49.366][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.366][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 19:17:49.366][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:49.367][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:49.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.368][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:49.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.369][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.369][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:49.369][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:49.370][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.370][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.370][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 19:17:49.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.371][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:49.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.371][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:49.372][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.373][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:49.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:49.373][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.373][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:49.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:49.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:49.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:49.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.376][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:49.377][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:49.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.377][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.378][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 19:17:49.378][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.378][self$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[2024-06-24 19:17:49.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:49.379][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.379][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.380][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.380][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.380][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:49.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:49.381][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.381][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 19:17:49.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:49.381][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.382][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.382][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.382][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:49.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:49.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.384][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:49.384][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:49.384][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.385][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.385][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 19:17:49.385][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.386][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:49.386][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:49.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.387][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.387][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:49.388][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:49.388][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.388][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 19:17:49.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:49.393][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.394][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.394][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.394][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:49.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.395][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:49.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.396][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:49.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:49.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.397][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:49.397][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:49.397][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.399][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[2024-06-24 19:17:49.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.401][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[2024-06-24 19:17:49.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.402][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[2024-06-24 19:17:49.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.414][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[2024-06-24 19:17:49.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.416][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 19:17:49.417][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 19:17:49.417][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 19:17:49.417][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 19:17:49.418][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:49.418][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 19:17:49.418][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:49.419][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:49.419][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 19:17:49.420][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 19:17:49.420][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:49.420][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 19:17:49.421][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:49.421][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:49.421][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 19:17:49.422][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 19:17:49.422][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 19:17:49.422][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 19:17:49.423][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:49.423][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 19:17:49.424][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 19:17:49.424][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 19:17:49.424][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 19:17:49.425][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 19:17:49.425][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 19:17:49.425][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 19:17:49.426][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 19:17:49.426][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 19:17:49.427][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 19:17:49.427][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 19:17:49.427][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 19:17:49.428][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 19:17:49.428][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 19:17:49.428][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 19:17:49.429][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 19:17:49.429][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 19:17:49.429][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 19:17:49.430][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 19:17:49.430][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 19:17:49.430][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 19:17:49.431][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 19:17:49.431][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 19:17:49.432][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 19:17:49.432][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 19:17:49.432][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 19:17:49.433][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 19:17:49.433][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 19:17:49.433][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 19:17:49.434][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 19:17:49.434][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 19:17:49.434][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 19:17:49.435][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 19:17:49.435][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 19:17:49.436][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 19:17:49.436][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 19:17:49.436][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 19:17:49.437][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 19:17:49.437][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 19:17:49.437][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 19:17:49.438][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 19:17:49.438][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 19:17:49.438][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 19:17:49.439][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 19:17:49.439][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 19:17:49.439][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 19:17:49.440][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 19:17:49.440][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:49.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:49.441][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 19:17:49.441][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 19:17:49.442][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 19:17:49.442][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 19:17:49.442][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 19:17:49.443][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 19:17:49.443][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 19:17:49.443][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 19:17:49.444][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 19:17:49.444][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 19:17:49.444][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 19:17:49.445][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 19:17:49.445][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 19:17:49.446][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 19:17:49.446][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 19:17:49.446][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 19:17:49.447][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:49.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:49.447][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.448][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.450][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[2024-06-24 19:17:49.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.462][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.DEBUG[2024-06-24 19:17:49.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.465][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[2024-06-24 19:17:49.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.468][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[2024-06-24 19:17:49.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:49.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:49.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:49.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:49.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:49.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:49.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:49.477][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:49.477][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 19:17:49.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.478][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:49.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.479][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.480][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 19:17:49.480][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 19:17:49.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:49.480][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 19:17:49.481][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 19:17:49.482][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:49.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:49.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:49.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:49.484][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:49.484][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 19:17:49.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:49.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:49.484][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:49.485][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 19:17:49.485][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 19:17:49.485][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:49.485][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:49.486][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 19:17:49.486][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:49.487][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:49.487][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:49.488][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 19:17:49.488][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 19:17:49.489][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 19:17:49.489][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 19:17:49.489][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:49.490][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:49.490][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 19:17:49.490][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 19:17:49.491][biodb::testThat]
biodb.INFO [2024-06-24 19:17:49.491][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-24 19:17:49.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:49.491][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:49.492][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 19:17:49.493][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:49.494][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 19:17:49.494][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:49.494][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 19:17:49.495][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 19:17:49.496][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:49.497][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:49.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 19:17:49.832][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 19:17:50.161][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:50.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-24 19:17:50.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-24 19:17:50.166][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 19:17:50.166][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 19:17:50.166][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 19:17:50.167][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 19:17:50.167][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.167][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.168][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 19:17:50.169][biodb::testContext]
biodb.INFO [2024-06-24 19:17:50.169][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:50.169][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-24 19:17:50.169][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 19:17:50.170][biodb::testContext]
biodb.INFO [2024-06-24 19:17:50.170][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:50.171][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:50.172][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:50.172][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 19:17:50.173][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.173][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 19:17:50.174][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.175][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 19:17:50.175][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.176][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 19:17:50.176][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 19:17:50.176][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 19:17:50.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.177][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 19:17:50.177][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 19:17:50.177][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.178][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 19:17:50.178][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 19:17:50.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.179][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 19:17:50.179][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 19:17:50.180][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 19:17:50.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 19:17:50.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.181][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[2024-06-24 19:17:50.181][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 19:17:50.182][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 19:17:50.182][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 19:17:50.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.183][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:50.183][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 19:17:50.183][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 19:17:50.183][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 19:17:50.183][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 19:17:50.184][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 19:17:50.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.184][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 19:17:50.185][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 19:17:50.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.185][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 19:17:50.186][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 19:17:50.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.186][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 19:17:50.187][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 19:17:50.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.187][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 19:17:50.188][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 19:17:50.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.188][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 19:17:50.189][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 19:17:50.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.189][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 19:17:50.190][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 19:17:50.195][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 19:17:50.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.195][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 19:17:50.196][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 19:17:50.196][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 19:17:50.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.197][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 19:17:50.197][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.197][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 19:17:50.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:50.198][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.199][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:50.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:50.199][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.200][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 19:17:50.200][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:50.200][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.200][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.201][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:50.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.202][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.202][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:50.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:50.203][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.203][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.203][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 19:17:50.204][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.204][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:50.204][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.204][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:50.205][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.205][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.205][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.205][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.206][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:50.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:50.206][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.206][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 19:17:50.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 19:17:50.207][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:50.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:50.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.209][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.209][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.209][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:50.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:50.209][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.210][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.210][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 19:17:50.210][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.210][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 19:17:50.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:50.211][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.211][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.212][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.212][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.212][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 19:17:50.212][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:50.212][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.213][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 19:17:50.213][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:50.213][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.213][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.214][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.214][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:50.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:50.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.215][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.215][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:50.216][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:50.216][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.216][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.216][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 19:17:50.217][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.217][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 19:17:50.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.217][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:50.218][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.218][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.218][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.218][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 19:17:50.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:50.219][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.219][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 19:17:50.219][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:50.220][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.220][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.220][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.220][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 19:17:50.220][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.221][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:50.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.221][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.222][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.222][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:50.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:50.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.222][self$setPropertyValue]
biodb.DEBUG[2024-06-24 19:17:50.223][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:50.223][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.223][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.DEBUG[2024-06-24 19:17:50.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.228][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[2024-06-24 19:17:50.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.229][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[2024-06-24 19:17:50.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.230][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[2024-06-24 19:17:50.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.238][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[2024-06-24 19:17:50.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.242][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[2024-06-24 19:17:50.242][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 19:17:50.243][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 19:17:50.243][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 19:17:50.243][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 19:17:50.244][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:50.244][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 19:17:50.244][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:50.245][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:50.245][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 19:17:50.245][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 19:17:50.245][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:50.246][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 19:17:50.246][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 19:17:50.246][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 19:17:50.247][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 19:17:50.247][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 19:17:50.247][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 19:17:50.248][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 19:17:50.248][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:50.248][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 19:17:50.249][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 19:17:50.249][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 19:17:50.249][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 19:17:50.250][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 19:17:50.250][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 19:17:50.250][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 19:17:50.250][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 19:17:50.251][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 19:17:50.251][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 19:17:50.251][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 19:17:50.252][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 19:17:50.252][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 19:17:50.252][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 19:17:50.253][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 19:17:50.253][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 19:17:50.253][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 19:17:50.254][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 19:17:50.254][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 19:17:50.254][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 19:17:50.255][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 19:17:50.255][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 19:17:50.255][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 19:17:50.255][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 19:17:50.256][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 19:17:50.256][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 19:17:50.256][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 19:17:50.257][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 19:17:50.257][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 19:17:50.257][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 19:17:50.258][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 19:17:50.258][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 19:17:50.258][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 19:17:50.259][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 19:17:50.259][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 19:17:50.259][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 19:17:50.259][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 19:17:50.260][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 19:17:50.260][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 19:17:50.260][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 19:17:50.261][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 19:17:50.261][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 19:17:50.261][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 19:17:50.262][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 19:17:50.262][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 19:17:50.262][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 19:17:50.263][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 19:17:50.263][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:50.263][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:50.263][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 19:17:50.264][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 19:17:50.264][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 19:17:50.264][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 19:17:50.265][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 19:17:50.265][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 19:17:50.265][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 19:17:50.266][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 19:17:50.266][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 19:17:50.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 19:17:50.267][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 19:17:50.267][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 19:17:50.267][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 19:17:50.267][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 19:17:50.268][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 19:17:50.268][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 19:17:50.269][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-24 19:17:50.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 19:17:50.269][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.269][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.272][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.DEBUG[2024-06-24 19:17:50.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.286][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[2024-06-24 19:17:50.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.288][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[2024-06-24 19:17:50.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 19:17:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.293][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 19:17:50.293][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 19:17:50.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.294][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.294][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.294][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 19:17:50.294][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.295][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.295][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.295][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 19:17:50.297][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 19:17:50.298][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 19:17:50.299][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 19:17:50.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 19:17:50.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 19:17:50.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 19:17:50.301][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 19:17:50.301][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 19:17:50.302][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 19:17:50.302][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 19:17:50.302][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 19:17:50.303][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 19:17:50.303][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 19:17:50.303][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 19:17:50.304][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 19:17:50.305][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 19:17:50.305][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 19:17:50.305][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 19:17:50.305][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:50.306][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 19:17:50.306][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 19:17:50.306][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 19:17:50.307][biodb::testThat]
biodb.INFO [2024-06-24 19:17:50.307][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-24 19:17:50.307][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 19:17:50.307][biodb::testThat]
biodb.DEBUG[2024-06-24 19:17:50.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 19:17:50.309][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:50.309][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 19:17:50.310][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:50.310][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 19:17:50.311][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[2024-06-24 19:17:50.312][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 19:17:50.312][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-24 19:17:50.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 19:17:50.313][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-24 19:17:50.314][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-24 19:17:50.314][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 19:17:50.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-24 19:17:50.315][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 19:17:50.315][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 19:17:50.315][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 19:17:50.315][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 19:17:50.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 19:17:50.316][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 19:17:50.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:50.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:50.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:50.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:50.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:50.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:50.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 19:17:50.319][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-24 19:17:50.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 19:17:50.320][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 19:17:50.320][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-24 19:17:50.656][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-24 19:17:51.618][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 19:17:51.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-24 19:17:51.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-24 19:17:51.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-24 19:17:51.621][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 19:17:51.621][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 19:17:51.621][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 19:17:51.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 19:17:51.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:51.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:51.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:51.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:51.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:51.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 19:17:51.626][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.626][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.628][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:51.629][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:51.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.629][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.629][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 19:17:51.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 19:17:51.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.630][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:51.631][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:51.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.631][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 19:17:51.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 19:17:51.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.632][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 19:17:51.633][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 19:17:51.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.633][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.634][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 19:17:51.634][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 19:17:51.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.634][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.635][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:51.635][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:51.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.635][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.636][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:51.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 19:17:51.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.637][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:51.637][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:51.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.637][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.638][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 19:17:51.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 19:17:51.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.639][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:51.639][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:51.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.639][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:51.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 19:17:51.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.641][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:51.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:51.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 19:17:51.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 19:17:51.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.643][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:51.643][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:51.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.643][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 19:17:51.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 19:17:51.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.645][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:51.645][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:51.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 19:17:51.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 19:17:51.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 19:17:51.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 19:17:51.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 19:17:51.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 19:17:51.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 19:17:51.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 19:17:51.656][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-24 19:17:51.657][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 19:17:51.658][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 19:17:51.658][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 19:17:51.658][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 19:17:51.658][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 19:17:51.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 19:17:51.659][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 19:17:51.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 19:17:51.659][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 19:17:51.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
4.964 0.294 39.105
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 0.737 | 0.214 | 2.125 | |
| ChebiEntry | 0.113 | 0.006 | 0.119 | |