Pierrick Roger
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_19 |
| git_last_commit: fad38a4 |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz |
| StartedAt: 2024-06-27 01:08:44 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 01:12:11 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 206.7 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 4.948 2.353 10.683
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-06-27 01:10:27.438][biodb::testContext]
biodb.INFO [2024-06-27 01:10:27.446][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:10:27.450][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-27 01:10:27.452][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:10:27.455][biodb::testContext]
biodb.INFO [2024-06-27 01:10:27.473][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:10:27.477][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 01:10:27.496][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:10:27.498][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 01:10:27.503][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.516][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 01:10:27.584][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.596][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 01:10:27.599][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.613][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 01:10:27.616][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 01:10:27.619][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 01:10:27.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.649][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 01:10:27.654][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 01:10:27.657][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.667][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 01:10:27.669][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 01:10:27.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.679][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 01:10:27.681][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 01:10:27.683][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 01:10:27.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.692][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 01:10:27.694][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.704][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 01:10:27.706][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 01:10:27.709][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 01:10:27.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.718][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:10:27.720][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 01:10:27.722][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 01:10:27.725][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 01:10:27.729][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 01:10:27.732][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 01:10:27.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.742][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 01:10:27.745][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 01:10:27.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.755][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 01:10:27.758][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 01:10:27.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.767][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 01:10:27.769][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 01:10:27.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.778][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 01:10:27.781][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 01:10:27.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.790][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 01:10:27.793][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 01:10:27.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.803][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:10:27.805][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 01:10:27.827][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 01:10:27.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.837][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 01:10:27.839][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 01:10:27.842][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 01:10:27.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:27.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:27.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:27.856][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 01:10:27.954][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.001][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-27 01:10:28.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:10:28.008][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.012][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.014][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.019][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:10:28.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:10:28.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.026][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 01:10:28.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:10:28.032][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.037][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:10:28.037][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:10:28.037][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:10:28.037][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:10:28.037][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:10:28.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:10:28.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:10:28.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.055][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.057][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:10:28.061][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:10:28.063][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.066][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.069][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 01:10:28.073][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.075][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:10:28.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:10:28.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.085][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.087][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.089][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.092][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:10:28.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:10:28.097][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.099][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 01:10:28.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:10:28.103][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.108][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:10:28.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:10:28.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:10:28.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:10:28.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:10:28.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:10:28.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:10:28.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.131][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:10:28.135][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:10:28.137][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.140][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.143][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 01:10:28.148][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-27 01:10:28.153][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:10:28.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.165][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.178][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:10:28.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:10:28.182][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.185][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 01:10:28.188][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:10:28.190][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.193][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.196][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.198][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:10:28.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.206][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:10:28.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.213][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.215][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:10:28.220][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:10:28.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.224][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.227][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 01:10:28.231][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.235][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:10:28.238][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:10:28.242][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.245][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.247][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.252][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:10:28.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:10:28.257][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.260][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 01:10:28.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:10:28.265][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.268][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:28.270][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.273][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:10:28.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:10:28.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:28.286][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:28.288][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:10:28.292][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:10:28.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:10:28.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:28.301][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:10:28.310][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:10:28.312][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.315][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[2024-06-27 01:10:28.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.337][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[2024-06-27 01:10:28.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.370][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[2024-06-27 01:10:28.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.381][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[2024-06-27 01:10:28.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.404][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[2024-06-27 01:10:28.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.415][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[2024-06-27 01:10:28.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.439][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[2024-06-27 01:10:28.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.450][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[2024-06-27 01:10:28.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.471][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[2024-06-27 01:10:28.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.510][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 01:10:28.519][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 01:10:28.522][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 01:10:28.526][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 01:10:28.530][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:10:28.537][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 01:10:28.542][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 01:10:28.546][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 01:10:28.550][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 01:10:28.553][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 01:10:28.557][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:10:28.560][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 01:10:28.564][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 01:10:28.568][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 01:10:28.572][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 01:10:28.575][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 01:10:28.580][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 01:10:28.583][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 01:10:28.586][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:10:28.590][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 01:10:28.594][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 01:10:28.598][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 01:10:28.602][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 01:10:28.605][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 01:10:28.609][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 01:10:28.613][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 01:10:28.617][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 01:10:28.624][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 01:10:28.628][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 01:10:28.637][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 01:10:28.640][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 01:10:28.644][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 01:10:28.647][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 01:10:28.651][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 01:10:28.654][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 01:10:28.659][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 01:10:28.662][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 01:10:28.666][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 01:10:28.670][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 01:10:28.673][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 01:10:28.679][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 01:10:28.682][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 01:10:28.687][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 01:10:28.692][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 01:10:28.704][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 01:10:28.708][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 01:10:28.712][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 01:10:28.715][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 01:10:28.719][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 01:10:28.722][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 01:10:28.726][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 01:10:28.729][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 01:10:28.733][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 01:10:28.737][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 01:10:28.742][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 01:10:28.745][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 01:10:28.749][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 01:10:28.752][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 01:10:28.756][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 01:10:28.760][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 01:10:28.763][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 01:10:28.768][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 01:10:28.771][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 01:10:28.775][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 01:10:28.778][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 01:10:28.782][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 01:10:28.788][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:10:28.792][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:10:28.797][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 01:10:28.801][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 01:10:28.805][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 01:10:28.812][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 01:10:28.816][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 01:10:28.820][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 01:10:28.824][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 01:10:28.827][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 01:10:28.830][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 01:10:28.834][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 01:10:28.837][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 01:10:28.841][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 01:10:28.846][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 01:10:28.850][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 01:10:28.855][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 01:10:28.874][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 01:10:28.880][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:10:28.886][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:10:28.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.894][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:28.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:28.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:28.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:28.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:28.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:28.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:28.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:28.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:28.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:28.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:28.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:28.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:28.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.002][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[2024-06-27 01:10:29.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.019][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.DEBUG[2024-06-27 01:10:29.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:29.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.054][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[2024-06-27 01:10:29.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.071][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[2024-06-27 01:10:29.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.085][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[2024-06-27 01:10:29.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.100][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[2024-06-27 01:10:29.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:29.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:29.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.148][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.DEBUG[2024-06-27 01:10:29.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:29.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.185][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[2024-06-27 01:10:29.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:10:29.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:29.205][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-27 01:10:29.242][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-27 01:10:29.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:29.250][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 01:10:29.252][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:29.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:10:29.259][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:29.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:10:29.264][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:29.267][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-27 01:10:29.270][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-27 01:10:29.272][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:10:29.276][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:29.279][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-27 01:10:29.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-27 01:10:29.285][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-27 01:10:29.290][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 01:10:29.292][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:10:29.292][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:10:29.292][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:10:29.295][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-27 01:10:29.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:29.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:29.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:10:29.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:10:29.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:10:29.311][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:10:29.314][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:29.314][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-27 01:10:29.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:10:29.319][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:10:29.324][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 01:10:29.327][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-27 01:10:29.327][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-27 01:10:29.346][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:10:29.353][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:10:29.357][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-27 01:10:29.361][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:10:29.365][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:10:29.369][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:10:29.423][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-27 01:10:29.427][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-27 01:10:29.438][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-27 01:10:29.448][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-27 01:10:29.458][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:10:29.462][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:10:29.465][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-27 01:10:29.467][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-27 01:10:29.489][biodb::testThat]
biodb.INFO [2024-06-27 01:10:29.491][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-27 01:10:29.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:29.496][biodb::testThat]
biodb.TRACE[2024-06-27 01:10:29.505][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-27 01:10:29.509][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:29.517][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:29.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:29.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:29.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:29.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:29.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:29.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:29.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:29.606][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:29.609][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:29.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.614][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:29.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:29.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.665][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:29.668][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:29.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.674][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.759][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.770][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:29.773][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:29.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:29.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.810][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:29.812][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:29.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.816][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:29.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:29.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.833][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:29.836][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:29.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.843][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:29.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.858][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:29.860][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:29.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.870][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:29.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:29.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.881][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:29.884][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:29.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:29.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:29.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.902][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:29.904][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:29.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.910][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:29.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:29.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.923][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:29.925][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:29.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:29.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:29.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.946][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:29.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:29.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.957][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:29.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:29.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.967][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:29.970][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:29.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:29.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:29.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:29.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:29.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:30.205][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-27 01:10:30.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:30.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:30.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:30.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:30.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:30.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:30.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:30.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:30.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:30.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:30.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.389][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:30.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:30.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:30.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:30.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:30.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:30.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.714][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:30.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.806][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.809][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:30.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:30.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:30.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:30.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:30.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.885][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:30.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:30.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.893][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:30.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:30.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:30.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:30.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.951][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:30.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:30.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.963][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:30.966][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:30.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:30.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:30.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:30.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.044][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.047][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.124][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.161][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.187][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.207][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.220][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.286][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.289][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.295][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.328][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.339][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.369][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.402][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.413][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.433][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.436][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.508][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.516][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.582][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.591][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.623][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:31.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:31.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.651][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:31.654][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:31.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.658][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.670][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:31.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:31.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.678][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.690][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:31.693][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:31.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.697][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.709][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:31.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.728][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.732][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:31.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.748][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:31.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.755][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.770][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:31.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.775][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.786][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:31.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.805][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:31.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:31.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.813][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:31.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:31.826][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:31.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:31.831][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 01:10:31.852][biodb::testThat]
biodb.INFO [2024-06-27 01:10:31.855][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-27 01:10:31.857][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:31.860][biodb::testThat]
biodb.DEBUG[2024-06-27 01:10:31.900][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-27 01:10:31.915][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:31.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-27 01:10:31.927][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:31.930][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-27 01:10:31.933][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:32.009][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:32.012][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:32.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:32.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:32.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:32.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:32.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:32.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:32.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:32.045][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.125][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:32.128][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:32.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.133][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.146][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:32.148][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:32.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.153][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:32.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.166][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:32.169][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:32.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.175][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:32.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:32.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.188][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:32.190][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:32.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.196][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.210][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:32.213][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:32.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:32.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.231][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:32.234][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:32.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.241][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:32.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:32.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:32.255][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:32.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:32.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:32.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.273][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.276][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.281][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.284][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.296][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:32.298][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:32.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.307][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:32.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.317][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:32.320][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:32.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.325][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:32.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:32.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:32.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:32.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:32.446][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-27 01:10:32.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-27 01:10:32.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-27 01:10:32.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-27 01:10:32.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-27 01:10:32.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-27 01:10:32.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-27 01:10:32.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:10:32.506][biodb::testThat]
biodb.INFO [2024-06-27 01:10:32.508][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-27 01:10:32.510][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:32.513][biodb::testThat]
biodb.TRACE[2024-06-27 01:10:32.520][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.527][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:32.530][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-27 01:10:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:32.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:32.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:32.647][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-27 01:10:32.659][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-27 01:10:32.716][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:10:32.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-27 01:10:32.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:32.769][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-27 01:10:32.840][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[2024-06-27 01:10:32.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:32.851][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:32.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:10:33.734][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:10:34.286][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:34.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-27 01:10:34.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-27 01:10:34.336][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-27 01:10:34.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:34.368][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:34.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.372][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.374][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.397][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.401][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 01:10:34.411][biodb::testThat]
biodb.INFO [2024-06-27 01:10:34.413][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-27 01:10:34.415][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:34.417][biodb::testThat]
biodb.TRACE[2024-06-27 01:10:34.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:34.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:34.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:34.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:34.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:34.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:34.663][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:10:34.672][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:10:34.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:10:34.679][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:34.682][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-27 01:10:34.729][biodb::testThat]
biodb.INFO [2024-06-27 01:10:34.732][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-27 01:10:34.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:34.737][biodb::testThat]
biodb.TRACE[2024-06-27 01:10:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:34.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:34.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.815][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:34.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:34.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:34.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:34.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:34.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:34.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:34.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:34.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:34.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:34.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:34.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:34.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:34.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:35.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:35.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:35.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:35.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:35.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:35.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 01:10:35.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 01:10:35.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:35.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 01:10:35.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:35.074][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:35.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 01:10:35.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:35.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:10:35.100][biodb::testThat]
biodb.INFO [2024-06-27 01:10:35.102][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-27 01:10:35.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:35.107][biodb::testThat]
biodb.INFO [2024-06-27 01:10:35.127][biodb::testThat]
biodb.INFO [2024-06-27 01:10:35.130][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-27 01:10:35.132][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:35.135][biodb::testThat]
biodb.INFO [2024-06-27 01:10:35.156][biodb::testThat]
biodb.INFO [2024-06-27 01:10:35.159][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-27 01:10:35.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:35.165][biodb::testThat]
biodb.DEBUG[2024-06-27 01:10:35.178][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-27 01:10:35.759][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-27 01:10:36.650][biodb::testThat]
biodb.INFO [2024-06-27 01:10:36.653][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-27 01:10:36.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:36.657][biodb::testThat]
biodb.DEBUG[2024-06-27 01:10:37.104][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[2024-06-27 01:10:37.547][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:37.550][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:37.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:37.554][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:37.556][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:37.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:37.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:37.563][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 01:10:37.567][biodb::testThat]
biodb.INFO [2024-06-27 01:10:37.569][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-06-27 01:10:37.571][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:10:37.573][biodb::testThat]
biodb.TRACE[2024-06-27 01:10:37.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:37.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:37.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:37.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:37.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:37.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:37.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:37.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:37.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:37.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:37.830][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:10:37.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:10:37.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:10:37.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:37.847][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-27 01:10:38.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:10:38.055][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:10:38.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:10:38.064][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:38.068][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-27 01:10:38.116][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 01:10:38.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 01:10:38.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:38.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:38.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:38.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:38.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:38.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:38.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:38.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:38.215][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:10:38.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:38.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:38.333][private$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[2024-06-27 01:10:38.754][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[2024-06-27 01:10:39.174][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:39.178][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-27 01:10:39.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-27 01:10:39.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:39.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:39.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:39.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:39.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:39.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:39.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:39.218][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-27 01:10:39.355][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:39.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-27 01:10:39.362][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:39.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:39.367][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:39.370][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:39.372][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:39.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:39.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:39.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:39.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:39.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:39.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:39.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:39.408][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[2024-06-27 01:10:39.411][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-27 01:10:39.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:39.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:39.439][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-27 01:10:39.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-27 01:10:40.313][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:40.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-27 01:10:40.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-27 01:10:40.331][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-27 01:10:40.335][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:40.338][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:40.341][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:40.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:40.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:40.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:40.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:40.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:40.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:40.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:40.371][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.390][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:40.393][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:40.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.398][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.401][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:40.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:40.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.411][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:40.414][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:40.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.419][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:40.435][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:40.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:40.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:40.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.452][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:40.454][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:40.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.458][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:40.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:40.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.478][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.481][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:40.484][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:40.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:40.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:40.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:40.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:40.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.520][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:40.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:40.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.528][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:40.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:40.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:40.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:40.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.551][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:40.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:40.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.563][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:40.565][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:40.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.648][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:40.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:40.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:40.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:40.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:40.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:40.771][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-27 01:10:40.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:40.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:40.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:40.833][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[2024-06-27 01:10:40.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:40.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:40.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:10:41.258][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:10:41.711][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:41.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-27 01:10:41.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-27 01:10:41.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:41.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:41.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:41.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:41.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:41.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:41.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:41.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:41.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:41.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:41.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:41.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:41.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:41.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:41.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:41.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:41.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:41.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:41.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:41.866][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-27 01:10:41.868][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:41.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-27 01:10:41.875][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:41.877][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:41.880][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:41.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:41.885][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:41.888][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:41.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:41.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:41.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:41.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:41.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:41.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:41.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:41.948][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-27 01:10:41.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:41.957][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:41.960][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-27 01:10:42.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-27 01:10:42.796][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:42.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-27 01:10:42.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-27 01:10:42.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-27 01:10:42.850][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:42.853][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:42.856][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:42.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:42.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:42.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:42.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:42.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:42.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:42.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:42.890][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:42.893][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:42.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:42.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.910][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:42.913][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:42.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.917][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.920][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:42.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:42.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.943][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:42.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:42.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:42.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:42.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:42.965][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:42.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:42.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:42.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.982][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:42.984][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:42.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:42.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:42.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:42.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.001][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:43.004][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:43.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.011][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:43.013][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.020][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:43.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:43.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.038][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:43.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:43.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.053][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:43.055][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:43.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.060][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:43.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:43.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.074][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:43.076][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:43.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:43.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:43.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.094][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:43.096][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:43.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.104][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:43.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:43.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:43.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:43.235][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-27 01:10:43.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:43.324][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:10:43.337][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:10:43.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:10:43.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:10:43.349][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-27 01:10:43.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:43.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:43.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:43.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:43.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:43.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:43.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:43.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:43.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:43.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:43.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:43.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:43.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:43.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:43.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:43.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:43.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:43.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:43.442][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-27 01:10:43.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:43.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-27 01:10:43.452][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:43.455][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:43.458][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:43.460][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:43.463][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:43.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:43.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:43.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:43.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:43.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:43.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:43.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:43.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:43.500][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-27 01:10:43.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:43.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:43.513][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-27 01:10:43.919][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-27 01:10:44.329][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:44.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-27 01:10:44.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-27 01:10:44.386][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-27 01:10:44.390][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:44.393][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:44.396][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:44.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:44.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:44.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:44.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:44.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:44.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:44.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:44.428][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.448][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:44.451][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:44.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.459][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:44.461][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:44.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.466][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.469][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:44.472][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:44.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.478][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:44.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:44.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.485][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.488][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:44.490][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:44.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.495][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.498][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:44.500][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.507][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:44.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:44.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.514][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.517][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:44.520][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:44.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.524][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:44.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:44.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.537][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:44.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:44.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.544][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:44.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:44.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.558][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:44.560][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:44.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.565][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:44.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:44.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:44.678][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-27 01:10:44.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:44.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:44.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:44.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:44.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:44.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:44.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:44.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:44.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:44.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:44.765][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-27 01:10:44.768][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:44.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-27 01:10:44.776][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:44.779][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:44.782][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:44.784][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:44.787][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:44.790][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:44.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:44.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:44.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:44.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:44.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:44.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:44.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:44.822][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-27 01:10:44.828][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:44.830][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:44.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-27 01:10:45.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-27 01:10:45.657][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:45.661][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-27 01:10:45.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-27 01:10:45.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-27 01:10:45.680][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:45.683][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:45.686][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:45.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:45.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:45.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:45.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:45.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:45.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:45.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:45.718][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.721][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.739][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:45.742][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:45.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.750][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:45.753][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:45.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.758][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.775][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:45.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:45.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.789][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:45.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:45.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.796][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.799][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:45.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:45.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.806][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.809][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:45.812][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:45.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.817][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.820][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:45.823][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:45.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.830][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:45.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:45.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.837][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:45.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:45.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:45.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:45.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:45.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:45.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:45.876][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:45.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.881][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:45.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:45.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:45.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:45.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:45.989][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-27 01:10:45.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:45.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:45.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:46.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:46.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:46.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:46.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:46.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:46.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:46.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:46.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:46.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:46.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:46.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:46.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:46.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:46.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:46.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:46.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:46.110][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-27 01:10:46.112][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:46.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-27 01:10:46.121][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:46.124][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:46.127][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:46.129][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:46.132][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:46.134][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:46.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:46.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:46.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:46.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:46.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:46.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:46.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:46.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-27 01:10:46.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:46.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:46.183][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-27 01:10:46.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-27 01:10:47.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:47.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-27 01:10:47.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-27 01:10:47.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-27 01:10:47.030][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:47.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:47.036][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:47.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:47.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:47.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:47.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:47.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:47.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:47.062][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[2024-06-27 01:10:47.067][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.069][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.074][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.086][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:47.088][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:47.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.092][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.095][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:47.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:47.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:47.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:47.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:47.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:47.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.121][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.124][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:47.126][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:47.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.133][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:47.136][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.140][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:47.145][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:47.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.153][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:47.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:47.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.160][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:47.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:47.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.173][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:47.176][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:47.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:47.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.207][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:47.210][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:47.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:47.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:47.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:47.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:47.317][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-27 01:10:47.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:47.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:47.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:47.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:47.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:47.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:47.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:47.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:47.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:47.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:47.391][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-27 01:10:47.393][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:47.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-27 01:10:47.399][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:47.402][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:47.404][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:47.407][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:47.409][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:47.412][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:47.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:47.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:47.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:47.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:47.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:47.442][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:47.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:47.446][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-27 01:10:47.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:47.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:47.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-27 01:10:47.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-27 01:10:48.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:48.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-27 01:10:48.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-27 01:10:48.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-27 01:10:48.315][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:48.318][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:48.321][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:48.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:48.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:48.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:48.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:48.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:48.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:48.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:48.354][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.356][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.373][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:48.376][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:48.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.384][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:48.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:48.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.394][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:48.396][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:48.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.401][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:48.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:48.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.414][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:48.416][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:48.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.421][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:48.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:48.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.433][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:48.436][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:48.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:48.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:48.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.455][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:48.458][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:48.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.466][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:48.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:48.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.477][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:48.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.487][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:48.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.498][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:48.500][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:48.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:48.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:48.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.519][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:48.522][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:48.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:48.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:48.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.541][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:48.544][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:48.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.549][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:48.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:48.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.561][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:48.564][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:48.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.568][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.571][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:48.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:48.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:48.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:48.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:48.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:48.681][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-27 01:10:48.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:48.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:48.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:48.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:48.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:48.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:48.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:48.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:48.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:48.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:48.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:48.739][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-27 01:10:48.742][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:48.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-27 01:10:48.749][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:48.751][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:48.754][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:48.756][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:48.759][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:48.762][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:48.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:48.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:48.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:48.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:48.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:48.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:48.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:48.793][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-27 01:10:48.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:48.802][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:48.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-27 01:10:49.215][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-27 01:10:49.625][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:49.629][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-27 01:10:49.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-27 01:10:49.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-27 01:10:49.648][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:49.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:49.654][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:49.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:49.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:49.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:49.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:49.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:49.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:49.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:49.699][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:49.702][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:49.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.707][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:49.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:49.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.719][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:49.722][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:49.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:49.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.739][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:49.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:49.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:49.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:49.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:49.782][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:49.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:49.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:49.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:49.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.807][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.810][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:49.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.820][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:49.823][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:49.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.831][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:49.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:49.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.842][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:49.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:49.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:49.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.861][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:49.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:49.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.868][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:49.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.883][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:49.886][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:49.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.896][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.909][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:49.913][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:49.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.921][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:49.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:49.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:49.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:49.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:49.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:50.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:50.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:50.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:50.046][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-27 01:10:50.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:50.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:50.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:50.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:50.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:50.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:50.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:50.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:50.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:50.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:50.116][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-27 01:10:50.119][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:50.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-27 01:10:50.126][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:50.128][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:50.131][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:50.134][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:50.137][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:50.140][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:50.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:50.148][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:50.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:50.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:50.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:50.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:50.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:50.175][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-27 01:10:50.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:50.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:50.189][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-27 01:10:50.612][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-27 01:10:51.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:51.075][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-27 01:10:51.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-27 01:10:51.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-27 01:10:51.093][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:51.096][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:51.098][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:51.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:51.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:51.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:51.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:51.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:51.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:51.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:51.129][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.162][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:51.165][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:51.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.172][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:51.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.181][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:51.184][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:51.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.192][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:51.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:51.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.203][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:51.205][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:51.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:51.226][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:51.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.231][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:51.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:51.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.245][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:51.247][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:51.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.255][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:51.258][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.263][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:51.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.280][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:51.282][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:51.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.288][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:51.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:51.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.305][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:51.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:51.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.312][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:51.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:51.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.326][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:51.329][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:51.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.334][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.336][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:51.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:51.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.347][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:51.350][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:51.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.354][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:51.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:51.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:51.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:51.493][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-27 01:10:51.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:51.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:51.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:51.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:51.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:51.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:51.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:51.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:51.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:51.565][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-27 01:10:51.568][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:51.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-27 01:10:51.574][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:51.578][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:51.580][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:51.583][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:51.585][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:51.588][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:51.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:51.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:51.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:51.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:51.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:51.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:51.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:51.621][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-27 01:10:51.628][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:51.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:51.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-27 01:10:52.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-27 01:10:52.455][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:52.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-27 01:10:52.468][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-27 01:10:52.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-27 01:10:52.477][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:52.480][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:52.483][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:52.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:52.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:52.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:52.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:52.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:52.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:52.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:52.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.516][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.533][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:52.536][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:52.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.544][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:52.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.554][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:52.556][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:52.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.561][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.588][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:52.590][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:52.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.595][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:52.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:52.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.608][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:52.611][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:52.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.616][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:52.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.628][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:52.631][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:52.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.635][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.638][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:52.641][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.657][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:52.660][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:52.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.664][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:52.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.677][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:52.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:52.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.685][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:52.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.698][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:52.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:52.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.706][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.708][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:52.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:52.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.718][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:52.721][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:52.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.725][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:52.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:52.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:52.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:52.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:52.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:52.851][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-27 01:10:52.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:52.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:52.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:52.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:52.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:52.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:52.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:52.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:52.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:52.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:52.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:52.923][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-27 01:10:52.925][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:52.929][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-27 01:10:52.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:52.937][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:52.940][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:52.943][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:52.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:52.948][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:52.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:52.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:52.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:52.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:52.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:52.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:52.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:52.986][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-27 01:10:52.993][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:52.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:52.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-27 01:10:53.479][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-27 01:10:53.884][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:53.889][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-27 01:10:53.897][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-27 01:10:53.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-27 01:10:53.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:53.910][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:53.913][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:53.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:53.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:53.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:53.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:53.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:53.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:53.939][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[2024-06-27 01:10:53.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:53.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:53.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:53.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.962][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:53.964][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:53.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.968][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:53.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:53.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.980][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:53.983][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:53.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:53.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:53.999][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:54.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:54.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.006][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:54.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:54.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.018][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:54.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:54.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.024][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.049][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:54.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:54.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.056][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.059][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:54.061][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.069][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:54.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.078][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:54.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:54.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.085][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:54.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:54.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:54.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:54.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:54.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:54.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.116][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:54.119][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:54.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.123][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.126][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:54.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:54.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.135][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:54.137][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:54.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.142][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:54.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:54.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:54.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:54.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:54.253][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-27 01:10:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:54.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:54.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:54.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:54.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:54.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:54.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:54.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:54.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:54.318][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-27 01:10:54.321][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:54.324][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-27 01:10:54.327][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:54.330][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:54.332][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:54.335][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:54.337][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:54.339][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:54.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:54.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:54.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:54.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:54.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:54.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:54.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:54.371][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-27 01:10:54.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:54.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:54.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-27 01:10:54.794][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-27 01:10:55.211][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:55.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-27 01:10:55.223][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-27 01:10:55.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-27 01:10:55.233][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:55.236][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:55.239][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:55.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:55.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:55.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:55.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:55.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:55.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:55.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:55.269][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.272][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.275][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.286][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:55.288][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:55.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.292][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.295][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:55.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.305][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:55.308][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:55.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.312][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:55.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.324][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:55.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:55.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.331][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:55.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:55.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:55.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:55.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:55.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:55.364][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:55.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.371][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:55.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.377][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.380][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.402][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:55.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:55.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.409][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:55.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:55.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.424][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:55.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:55.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.431][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:55.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.443][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:55.446][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:55.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.450][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:55.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.464][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:55.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:55.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.472][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:55.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:55.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:55.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:55.590][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-27 01:10:55.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:55.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:55.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:55.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:55.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:55.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:55.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:55.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:55.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:55.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:55.653][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-27 01:10:55.655][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:55.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-27 01:10:55.666][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:55.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:55.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:55.674][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:55.677][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:55.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:55.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:55.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:55.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:55.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:55.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:55.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:55.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:55.718][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-27 01:10:55.725][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:55.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:55.731][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-27 01:10:56.136][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-27 01:10:56.555][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:56.560][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-27 01:10:56.569][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-27 01:10:56.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-27 01:10:56.579][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:56.582][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:56.585][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:56.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:56.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:56.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:56.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:56.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:56.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:56.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:56.617][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.620][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.641][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:56.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:56.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.649][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.652][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:56.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.664][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:56.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:56.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.672][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:56.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.685][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:56.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:56.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.692][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:56.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.704][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:56.706][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:56.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:56.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:56.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:56.726][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:56.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.733][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:56.736][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.743][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:56.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:56.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:56.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:56.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.773][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:56.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:56.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:56.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:56.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:56.809][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:56.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:56.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:56.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.827][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:56.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:56.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:56.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:56.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:56.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:56.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:56.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:56.948][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-27 01:10:56.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:56.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:56.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:56.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:56.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:56.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:56.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:57.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:57.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:57.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:57.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:57.012][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-27 01:10:57.015][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:57.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-27 01:10:57.022][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:57.025][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:57.028][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:57.031][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:57.034][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:57.036][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:57.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:57.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:57.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:57.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:57.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:57.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:57.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:57.068][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-27 01:10:57.074][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:57.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:57.088][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-27 01:10:57.499][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-27 01:10:57.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:57.913][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-27 01:10:57.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-27 01:10:57.928][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-27 01:10:57.932][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:57.935][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:57.938][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:57.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:57.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:57.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:57.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:57.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:57.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:57.967][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[2024-06-27 01:10:57.972][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:57.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:57.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:57.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:57.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:57.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:57.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:57.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:57.993][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:57.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:57.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.000][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:58.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:58.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.013][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:58.015][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:58.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.020][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:58.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:58.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.032][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:58.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:58.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.039][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.042][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:58.044][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:58.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.051][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:58.054][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:58.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.061][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:58.064][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.068][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.071][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:58.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.081][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:58.084][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:58.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:58.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:58.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.102][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:58.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:58.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.110][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:58.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:58.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.124][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:58.127][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:58.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.134][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:58.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:58.148][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:58.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:58.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:58.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:58.277][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-27 01:10:58.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:58.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:58.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:58.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:58.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:58.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:58.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:58.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:58.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:58.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:58.339][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-27 01:10:58.342][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:58.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-27 01:10:58.349][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:58.352][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:58.357][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:58.359][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:58.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:58.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:58.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:58.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:58.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:58.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:58.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:58.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:58.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:58.403][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-27 01:10:58.410][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:58.412][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:58.415][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-27 01:10:58.820][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-27 01:10:59.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:10:59.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-27 01:10:59.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-27 01:10:59.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-27 01:10:59.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:10:59.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:10:59.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:10:59.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:59.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:59.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:59.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:59.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:59.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:59.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:10:59.306][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.308][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.313][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.326][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:59.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:59.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.333][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:10:59.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:10:59.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.347][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:59.350][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:59.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.354][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:10:59.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:10:59.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.365][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:10:59.368][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:10:59.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.372][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.375][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:10:59.378][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:10:59.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.382][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.385][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:59.387][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:10:59.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.391][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.394][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:59.397][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.401][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.404][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:10:59.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.414][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:59.416][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:59.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.420][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:59.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:10:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.432][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:59.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:59.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:10:59.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:10:59.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:59.453][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:59.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.457][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:10:59.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:10:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.469][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:10:59.471][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:10:59.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:10:59.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:10:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:10:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:59.582][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-27 01:10:59.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:10:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:10:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:10:59.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:10:59.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:59.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:59.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:59.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:59.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:59.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:59.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:59.639][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-27 01:10:59.641][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:10:59.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-27 01:10:59.649][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:10:59.652][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:10:59.655][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:10:59.657][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:10:59.660][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:10:59.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:10:59.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:10:59.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:10:59.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:10:59.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:10:59.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:10:59.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:10:59.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:10:59.698][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-27 01:10:59.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:10:59.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:10:59.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-27 01:11:00.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-27 01:11:00.544][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:00.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-27 01:11:00.558][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-27 01:11:00.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-27 01:11:00.568][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:00.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:00.574][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:00.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:00.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:00.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:00.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:00.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:00.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:00.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:00.605][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.612][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.625][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:00.627][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:00.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.635][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:00.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:00.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.646][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:00.649][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:00.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.653][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:00.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:00.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:00.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:00.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:00.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:00.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:00.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.707][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:00.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:00.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.720][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:00.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:00.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.730][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:00.733][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:00.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:00.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:00.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.757][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.769][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:00.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:00.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.779][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:00.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:00.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.790][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:00.792][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:00.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.800][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:00.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:00.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.810][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:00.813][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:00.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.819][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:00.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:00.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:00.928][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-27 01:11:00.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:00.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:00.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:00.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:00.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:00.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:00.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:00.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:00.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:00.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:00.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:00.997][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-27 01:11:01.000][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:01.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-27 01:11:01.007][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:01.010][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:01.012][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:01.015][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:01.017][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:01.020][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:01.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:01.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:01.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:01.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:01.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:01.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:01.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:01.053][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-27 01:11:01.061][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:01.064][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:01.067][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-27 01:11:01.570][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-27 01:11:02.028][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:02.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-27 01:11:02.041][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-27 01:11:02.048][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-27 01:11:02.051][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:02.054][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:02.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:02.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:02.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:02.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:02.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:02.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:02.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:02.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:02.089][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.091][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.109][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:02.112][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:02.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.116][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:02.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.129][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:02.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:02.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:02.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:02.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.148][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:02.150][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:02.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.155][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.182][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:02.185][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:02.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:02.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.202][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:02.205][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:02.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.212][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:02.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.219][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.222][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:02.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:02.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:02.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.239][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:02.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:02.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.252][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:02.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:02.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.259][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:02.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:02.274][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:02.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.282][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:02.296][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:02.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.300][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:02.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:02.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:02.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:02.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:02.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:02.411][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-27 01:11:02.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:02.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:02.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:02.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:02.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:02.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:02.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:02.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:02.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:02.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:02.478][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-27 01:11:02.480][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:02.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-27 01:11:02.486][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:02.489][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:02.492][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:02.494][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:02.496][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:02.498][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:02.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:02.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:02.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:02.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:02.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:02.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:02.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:02.532][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-27 01:11:02.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:02.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:02.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-27 01:11:03.015][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-27 01:11:03.500][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:03.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-27 01:11:03.514][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-27 01:11:03.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-27 01:11:03.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:03.528][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:03.531][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:03.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:03.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:03.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:03.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:03.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:03.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:03.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:03.562][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.582][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:03.584][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:03.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.589][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.591][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:03.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:03.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.601][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:03.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:03.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.608][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:03.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:03.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.621][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:03.623][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:03.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.628][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:03.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:03.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.640][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:03.642][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:03.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.646][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:03.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:03.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.658][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:03.660][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:03.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.664][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.667][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:03.670][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.688][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.692][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:03.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:03.705][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:03.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.723][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:03.725][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:03.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.731][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:03.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:03.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.744][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:03.746][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:03.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.751][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.753][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:03.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.764][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:03.766][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:03.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.773][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:03.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:03.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:03.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:03.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:03.899][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-27 01:11:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:03.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:03.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:03.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:03.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:03.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:03.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:03.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:03.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:03.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:03.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:03.958][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-27 01:11:03.961][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:03.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-27 01:11:03.968][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:03.971][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:03.973][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:03.984][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:03.987][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:03.989][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:03.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:03.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:04.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:04.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:04.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:04.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:04.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:04.023][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-27 01:11:04.030][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:04.033][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:04.037][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-27 01:11:04.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-27 01:11:04.883][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:04.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-27 01:11:04.896][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-27 01:11:04.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-27 01:11:04.906][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:04.909][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:04.912][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:04.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:04.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:04.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:04.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:04.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:04.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:04.939][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[2024-06-27 01:11:04.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:04.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:04.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:04.951][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:04.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:04.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:04.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:04.965][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:04.967][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:04.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:04.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:04.975][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:04.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:04.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:04.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:04.985][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:04.988][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:04.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:04.992][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:04.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:04.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:04.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.004][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:05.007][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:05.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.011][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:05.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:05.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:05.027][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:05.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.032][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:05.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.045][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:05.048][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:05.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.053][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.055][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:05.058][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.065][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:05.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.075][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:05.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:05.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:05.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:05.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.095][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:05.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:05.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.117][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:05.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:05.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:05.136][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:05.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.140][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:05.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:05.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.154][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:05.157][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:05.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.162][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.166][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:05.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:05.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:05.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:05.281][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-27 01:11:05.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:05.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:05.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:05.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:05.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:05.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:05.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:05.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:05.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:05.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:05.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:05.342][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-27 01:11:05.346][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:05.350][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-27 01:11:05.354][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:05.357][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:05.360][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:05.364][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:05.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:05.369][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:05.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:05.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:05.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:05.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:05.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:05.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:05.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:05.413][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-27 01:11:05.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:05.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:05.426][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-27 01:11:05.847][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-27 01:11:06.252][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:06.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-27 01:11:06.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-27 01:11:06.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-27 01:11:06.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:06.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:06.280][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:06.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:06.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:06.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:06.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:06.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:06.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:06.308][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.TRACE[2024-06-27 01:11:06.313][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.316][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.320][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.332][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:06.334][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:06.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.339][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:06.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:06.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.352][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:06.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:06.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.359][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:06.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:06.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.372][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:06.374][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:06.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:06.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:06.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.392][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:06.394][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:06.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:06.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.412][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:06.414][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:06.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.419][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.422][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:06.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.429][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:06.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:06.445][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:06.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.450][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:06.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.462][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:06.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:06.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.469][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:06.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.482][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:06.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:06.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.492][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:06.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.519][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:06.523][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:06.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.527][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.532][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:06.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:06.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:06.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:06.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:06.649][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-27 01:11:06.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:06.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:06.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:06.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:06.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:06.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:06.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:06.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:06.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:06.710][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-27 01:11:06.712][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:06.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-27 01:11:06.720][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:06.723][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:06.726][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:06.729][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:06.732][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:06.735][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:06.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:06.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:06.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:06.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:06.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:06.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:06.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:06.768][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-27 01:11:06.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:06.778][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:06.783][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-27 01:11:07.197][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-27 01:11:07.609][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:07.614][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-27 01:11:07.631][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-27 01:11:07.644][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-27 01:11:07.648][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:07.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:07.654][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:07.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:07.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:07.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:07.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:07.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:07.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:07.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:07.687][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.711][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:07.714][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:07.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.719][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.722][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:07.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:07.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.733][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:07.735][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:07.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:07.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:07.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:07.756][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:07.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.760][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:07.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:07.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.772][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:07.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:07.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:07.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.792][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:07.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:07.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.801][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:07.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:07.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.808][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.811][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:07.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.821][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:07.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:07.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:07.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.841][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:07.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:07.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.860][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:07.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:07.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.870][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:07.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:07.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.879][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:07.882][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:07.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.887][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.890][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:07.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:07.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:07.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:07.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:07.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:07.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:08.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:08.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:08.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:08.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:08.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:08.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:08.014][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-27 01:11:08.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:08.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:08.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:08.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:08.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:08.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:08.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:08.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:08.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:08.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:08.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:08.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:08.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:08.074][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-27 01:11:08.076][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:08.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-27 01:11:08.083][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:08.086][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:08.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:08.091][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:08.095][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:08.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:08.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:08.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:08.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:08.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:08.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:08.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:08.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:08.132][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-27 01:11:08.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:08.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:08.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-27 01:11:08.547][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-27 01:11:08.960][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:08.964][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-27 01:11:08.973][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-27 01:11:08.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-27 01:11:08.982][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:08.985][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:08.988][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:08.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:08.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:08.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.034][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.037][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.055][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:09.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:09.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:09.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:09.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.074][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:09.077][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:09.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:09.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:09.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:09.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:09.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:09.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:09.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:09.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:09.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:09.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:09.134][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:09.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.138][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.141][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:09.143][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.150][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:09.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:09.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:09.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:09.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:09.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.187][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:09.190][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:09.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.197][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:09.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.211][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:09.213][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:09.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.221][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:09.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:09.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:09.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:09.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:09.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:09.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:09.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:09.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.390][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-27 01:11:09.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.473][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:09.482][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:09.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:11:09.489][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:09.492][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-27 01:11:09.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:09.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:09.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:09.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:09.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:09.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:09.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:09.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:09.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:09.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:09.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:10.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:10.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:10.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:10.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:10.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:10.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:10.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:10.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:10.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:10.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:10.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:10.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:11.023][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:11.032][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:11.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:11.039][private$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[2024-06-27 01:11:11.452][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[2024-06-27 01:11:11.855][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:11.860][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-27 01:11:11.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-27 01:11:11.878][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[2024-06-27 01:11:11.887][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:11.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:11.895][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:11:12.313][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:11:12.733][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:12.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-27 01:11:12.795][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-27 01:11:12.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:12.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:12.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:12.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:12.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:12.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:12.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:12.857][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-27 01:11:12.860][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:12.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-27 01:11:12.886][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:12.889][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:12.892][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:12.895][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:12.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:12.901][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:12.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:12.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:12.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:12.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:12.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:12.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:12.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:12.935][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-27 01:11:12.942][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:12.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:12.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-27 01:11:13.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-27 01:11:13.770][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:13.774][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-27 01:11:13.782][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-27 01:11:13.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-27 01:11:13.792][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:13.795][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:13.797][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:13.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:13.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:13.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:13.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:13.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:13.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:13.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:13.827][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:13.830][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:13.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.847][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:13.849][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:13.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.854][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:13.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.866][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:13.868][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:13.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.873][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:13.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:13.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.886][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:13.889][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:13.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.893][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:13.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:13.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.906][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:13.908][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:13.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:13.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.926][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:13.929][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:13.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.933][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.936][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.946][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:13.948][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:13.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:13.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:13.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.979][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:13.982][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:13.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:13.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:13.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.001][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:14.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:14.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:14.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.021][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:14.024][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:14.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.029][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.033][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:14.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:14.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.044][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:14.047][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:14.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.058][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:14.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:14.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:14.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:14.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:14.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:14.171][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-27 01:11:14.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:14.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:14.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:14.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:14.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:14.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:14.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:14.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:14.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:14.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:14.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:14.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:14.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:14.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:14.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:14.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:14.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:14.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:14.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:14.324][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-27 01:11:14.329][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:14.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-27 01:11:14.336][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:14.339][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:14.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:14.344][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:14.350][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:14.352][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:14.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:14.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:14.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:14.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:14.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:14.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:14.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:14.391][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-27 01:11:14.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:14.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:14.408][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-27 01:11:14.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-27 01:11:15.291][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:15.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-27 01:11:15.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-27 01:11:15.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-27 01:11:15.315][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:15.319][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:15.322][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:15.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:15.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:15.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:15.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:15.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:15.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:15.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:15.355][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.358][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.376][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:15.379][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:15.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.383][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:15.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.396][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:15.399][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:15.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.404][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:15.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.416][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:15.419][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:15.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.423][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:15.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:15.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.436][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:15.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:15.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.443][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:15.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.471][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:15.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:15.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.479][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.482][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:15.485][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:15.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.490][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.493][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:15.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:15.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.504][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.507][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.512][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.526][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:15.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:15.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.534][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:15.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.548][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:15.551][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:15.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.556][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:15.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:15.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.569][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:15.573][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:15.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.578][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:15.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:15.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:15.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:15.690][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-27 01:11:15.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:15.776][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:15.784][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:15.788][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:11:15.791][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:15.794][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-27 01:11:15.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:15.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:15.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:15.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:15.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:15.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:15.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:15.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:15.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:15.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:15.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:15.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:15.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:15.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:15.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:15.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:15.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:15.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:15.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:15.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:15.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:15.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:15.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:16.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:16.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:16.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:16.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:16.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:16.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:16.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:16.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:16.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:16.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:16.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.390][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:17.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:17.402][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-27 01:11:17.405][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:17.411][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-27 01:11:17.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:17.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:17.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:17.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:17.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:17.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:17.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:17.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:17.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:17.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:18.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.763][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:18.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:11:18.796][biodb::testThat]
biodb.INFO [2024-06-27 01:11:18.799][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-27 01:11:18.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:18.804][biodb::testThat]
biodb.TRACE[2024-06-27 01:11:18.811][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 01:11:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 01:11:18.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:18.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:18.917][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:18.920][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-27 01:11:18.923][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:18.927][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-27 01:11:18.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:18.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:18.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:18.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:18.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:18.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:18.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:18.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:18.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:18.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:18.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:18.995][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:19.004][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:19.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-27 01:11:19.010][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:19.014][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-27 01:11:19.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:19.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:19.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:19.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:19.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:19.143][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:19.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.205][private$selectFields]
biodb.TRACE[2024-06-27 01:11:19.207][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:19.209][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:19.211][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.214][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.217][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.233][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.241][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.243][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.251][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.310][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-27 01:11:19.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:19.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.362][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.365][private$selectFields]
biodb.TRACE[2024-06-27 01:11:19.367][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:19.370][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:19.373][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.379][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.384][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.402][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.405][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.407][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.413][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.416][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.457][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:19.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.518][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.523][private$selectFields]
biodb.TRACE[2024-06-27 01:11:19.526][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:19.528][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:19.531][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.536][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.544][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.547][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.552][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.555][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.557][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:19.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.570][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.572][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:19.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.615][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-27 01:11:19.619][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:19.621][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:19.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:19.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:19.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:19.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:19.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:19.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:19.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:19.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:19.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:19.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:19.908][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:19.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:19.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:19.924][private$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[2024-06-27 01:11:20.337][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[2024-06-27 01:11:20.745][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:20.749][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-27 01:11:20.759][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-27 01:11:20.767][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[2024-06-27 01:11:20.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:20.777][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:20.782][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:11:21.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:11:21.600][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:21.605][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-27 01:11:21.614][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-27 01:11:21.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:21.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:21.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:21.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:21.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:21.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:21.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:21.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:21.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:21.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:21.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:21.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:21.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:21.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:21.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:21.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:21.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:21.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:21.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:21.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:21.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:21.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:21.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:21.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:21.888][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:21.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:21.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:21.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:21.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:21.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:21.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:21.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:21.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:21.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:21.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:21.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:21.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:21.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:21.998][private$selectFields]
biodb.TRACE[2024-06-27 01:11:22.000][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:22.002][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:22.004][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.006][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.008][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.013][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.022][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.026][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.036][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.038][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:22.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.069][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-27 01:11:22.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.095][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.TRACE[2024-06-27 01:11:22.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.218][private$selectFields]
biodb.TRACE[2024-06-27 01:11:22.221][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:22.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:22.227][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.241][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.249][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.252][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.287][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.293][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.302][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.339][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:22.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:22.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.391][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.394][private$selectFields]
biodb.TRACE[2024-06-27 01:11:22.396][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:22.399][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:22.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.403][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.406][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.416][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.424][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.427][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.430][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.432][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.442][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:22.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.479][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-27 01:11:22.482][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:22.485][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:22.509][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:22.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:22.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:11:22.526][biodb::testThat]
biodb.INFO [2024-06-27 01:11:22.529][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-27 01:11:22.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:22.534][biodb::testThat]
biodb.TRACE[2024-06-27 01:11:22.542][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 01:11:22.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 01:11:22.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:22.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:22.640][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:22.649][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:22.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-27 01:11:22.656][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:22.659][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-27 01:11:22.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:22.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:22.725][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:22.735][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:22.739][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-27 01:11:22.742][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:22.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-27 01:11:22.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:22.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:22.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:22.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:22.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:22.864][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:22.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:22.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:22.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:22.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:22.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:22.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:22.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:22.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.915][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.918][private$selectFields]
biodb.TRACE[2024-06-27 01:11:22.920][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:22.923][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:22.925][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.928][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.951][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:22.953][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.964][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:22.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:22.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:22.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:22.998][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-27 01:11:23.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.047][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.049][private$selectFields]
biodb.TRACE[2024-06-27 01:11:23.052][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:23.054][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:23.058][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.060][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.064][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.068][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.071][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.073][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.079][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.081][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.085][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.095][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:23.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.133][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:23.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.183][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.185][private$selectFields]
biodb.TRACE[2024-06-27 01:11:23.187][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:23.190][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:23.192][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.195][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.214][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.219][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.224][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.229][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.231][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.269][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-27 01:11:23.271][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:23.273][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:23.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:23.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:23.374][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:23.382][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:23.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-27 01:11:23.388][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:23.392][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-27 01:11:23.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:23.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:23.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-27 01:11:23.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:23.417][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-27 01:11:23.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:23.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:23.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:23.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:23.611][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:23.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.670][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.673][private$selectFields]
biodb.TRACE[2024-06-27 01:11:23.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:23.679][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:23.682][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.699][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.703][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.708][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.721][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:23.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.759][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-27 01:11:23.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.786][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.TRACE[2024-06-27 01:11:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.810][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.813][private$selectFields]
biodb.TRACE[2024-06-27 01:11:23.815][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:23.818][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:23.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.833][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.836][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.843][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.849][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.851][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.862][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:23.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:23.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:23.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:23.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:23.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:23.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:23.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:23.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:23.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.965][private$selectFields]
biodb.TRACE[2024-06-27 01:11:23.967][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:23.970][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:23.973][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:23.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.978][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.984][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:23.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:23.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:23.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.001][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.003][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.008][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.011][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.019][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:24.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.063][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-27 01:11:24.065][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:24.068][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:24.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:24.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:24.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:11:24.108][biodb::testThat]
biodb.INFO [2024-06-27 01:11:24.111][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-27 01:11:24.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:24.116][biodb::testThat]
biodb.TRACE[2024-06-27 01:11:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 01:11:24.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 01:11:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:24.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:24.219][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:24.229][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:24.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-27 01:11:24.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:24.240][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-27 01:11:24.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:24.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:24.319][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:24.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-27 01:11:24.327][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:24.331][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-27 01:11:24.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:24.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:24.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:24.463][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:24.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.549][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.552][private$selectFields]
biodb.TRACE[2024-06-27 01:11:24.554][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:24.556][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:24.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.568][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.592][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.594][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.604][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:24.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.650][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-27 01:11:24.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.708][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.710][private$selectFields]
biodb.TRACE[2024-06-27 01:11:24.713][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:24.715][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:24.718][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.724][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.728][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.733][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.743][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.749][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.755][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.758][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.763][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.770][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.772][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.812][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:24.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:24.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:24.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:24.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:24.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:24.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:24.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:24.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.863][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.865][private$selectFields]
biodb.TRACE[2024-06-27 01:11:24.869][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:24.871][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:24.874][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.880][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.884][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.887][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.894][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.899][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:24.903][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.911][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.913][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:24.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:24.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:24.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:24.947][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-27 01:11:24.949][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:24.952][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:25.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:25.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:25.085][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:25.093][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:25.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-27 01:11:25.099][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:25.102][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-27 01:11:25.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:25.117][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:25.120][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-27 01:11:25.123][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:25.128][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-27 01:11:25.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:25.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:25.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:25.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:25.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:25.308][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 01:11:25.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.359][private$selectFields]
biodb.TRACE[2024-06-27 01:11:25.361][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:25.363][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:25.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.368][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.371][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.375][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.381][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.386][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.391][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.396][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.402][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.404][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.440][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-27 01:11:25.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.466][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.TRACE[2024-06-27 01:11:25.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.501][private$selectFields]
biodb.TRACE[2024-06-27 01:11:25.504][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:25.506][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:25.508][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.518][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.528][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.530][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.533][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.535][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.542][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.544][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.575][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-27 01:11:25.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:25.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.625][private$selectFields]
biodb.TRACE[2024-06-27 01:11:25.628][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 01:11:25.630][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 01:11:25.632][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.635][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.643][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.648][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.654][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.656][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.659][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-27 01:11:25.661][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.670][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-27 01:11:25.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:25.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:25.702][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-27 01:11:25.704][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 01:11:25.707][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 01:11:25.755][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:25.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 01:11:25.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:25.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 01:11:25.773][biodb::testThat]
biodb.INFO [2024-06-27 01:11:25.776][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-06-27 01:11:25.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:25.781][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:25.785][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-27 01:11:25.788][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:25.792][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-27 01:11:25.795][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:25.798][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:25.802][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:25.804][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:25.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:25.810][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:25.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:25.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:25.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:25.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:25.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:25.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:25.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:25.843][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-27 01:11:25.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:25.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:25.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-27 01:11:26.266][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-27 01:11:26.696][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:26.700][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-27 01:11:26.709][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-27 01:11:26.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-27 01:11:26.719][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:26.722][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:26.725][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:26.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:26.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:26.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:26.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:26.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:26.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:26.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:26.756][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.764][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.777][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:26.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:26.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.784][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:26.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:26.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.798][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:26.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:26.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.806][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.809][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:26.811][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:26.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.817][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.820][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:26.822][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:26.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.830][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:26.832][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:26.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.836][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.839][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:26.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:26.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.849][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:26.852][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:26.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.857][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.860][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:26.863][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:26.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.868][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.872][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:26.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:26.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.880][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:26.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:26.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:26.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:26.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:27.000][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-27 01:11:27.003][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-27 01:11:27.027][biodb::testThat]
biodb.INFO [2024-06-27 01:11:27.029][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-27 01:11:27.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:27.035][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:27.060][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-27 01:11:27.063][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-27 01:11:27.066][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-27 01:11:27.070][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-27 01:11:27.074][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-06-27 01:11:27.113][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-06-27 01:11:27.115][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:27.118][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:27.121][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:27.123][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:27.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:27.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:27.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:27.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:27.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:27.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:27.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:27.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-27 01:11:27.163][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:27.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:27.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-27 01:11:27.594][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-27 01:11:28.004][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:28.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-27 01:11:28.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-27 01:11:28.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:28.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:28.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:28.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:28.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:28.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:28.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:28.048][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-27 01:11:28.056][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:28.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:28.062][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-27 01:11:28.474][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-27 01:11:28.883][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:28.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-27 01:11:28.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-27 01:11:28.925][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-27 01:11:28.929][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:28.932][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-27 01:11:28.935][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:28.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:28.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:28.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:28.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:28.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:28.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:28.960][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[2024-06-27 01:11:28.965][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:28.968][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:28.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:28.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:28.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:28.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:28.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:28.985][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:28.988][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:28.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:28.992][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:28.995][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:28.997][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:29.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:29.008][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:29.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.018][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.023][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.025][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.028][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.032][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.035][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:29.038][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:29.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.045][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.047][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.052][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.055][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:29.057][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:29.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.065][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:29.068][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:29.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.075][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:29.078][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:29.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:29.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:29.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:29.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:29.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:29.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:29.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:29.173][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[2024-06-27 01:11:29.177][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.196][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:29.199][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:29.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.206][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:29.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.214][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:29.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:29.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:29.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:29.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:29.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.253][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.256][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.274][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.277][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.282][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.295][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:29.299][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:29.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.304][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:29.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.317][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.320][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.325][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.339][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:29.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:29.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:29.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.361][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:29.366][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:29.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.370][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.375][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.388][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:29.392][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:29.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.397][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.401][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:29.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:29.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:29.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:29.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:29.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:29.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:29.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:29.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:29.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:29.517][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.520][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.524][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.537][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:29.539][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:29.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.544][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:29.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:29.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.557][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:29.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:29.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.564][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:29.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:29.580][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:29.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:29.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.604][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.608][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:29.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.621][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.625][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.630][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:29.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.643][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:29.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:29.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.650][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.653][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:29.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:29.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.664][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.667][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.671][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:29.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.684][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:29.686][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:29.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.691][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:29.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.704][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:29.707][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:29.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.714][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.717][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:29.730][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:29.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:29.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.788][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:29.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:29.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:29.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:29.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:29.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:29.916][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-27 01:11:29.918][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-27 01:11:29.920][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-27 01:11:29.954][biodb::testThat]
biodb.INFO [2024-06-27 01:11:29.956][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-06-27 01:11:29.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:29.961][biodb::testThat]
biodb.INFO [2024-06-27 01:11:30.022][biodb::testThat]
biodb.INFO [2024-06-27 01:11:30.024][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-06-27 01:11:30.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:30.029][biodb::testThat]
biodb.INFO [2024-06-27 01:11:30.049][biodb::testThat]
biodb.INFO [2024-06-27 01:11:30.052][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-06-27 01:11:30.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:30.056][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:30.062][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[2024-06-27 01:11:30.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:30.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:30.078][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:11:30.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:11:31.161][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:31.166][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-27 01:11:31.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-27 01:11:31.207][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:31.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:31.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:31.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:31.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:31.221][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:31.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:31.225][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 01:11:31.229][biodb::testThat]
biodb.INFO [2024-06-27 01:11:31.231][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-27 01:11:31.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:31.236][biodb::testThat]
biodb.ERROR[2024-06-27 01:11:31.268][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-27 01:11:31.307][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-27 01:11:31.340][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 01:11:31.342][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-27 01:11:31.345][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-27 01:11:31.347][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 01:11:31.349][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:31.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:31.354][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:31.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:31.358][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 01:11:31.389][biodb::testContext]
biodb.INFO [2024-06-27 01:11:31.391][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:31.394][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-27 01:11:31.396][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:31.399][biodb::testContext]
biodb.INFO [2024-06-27 01:11:31.404][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:31.409][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:31.417][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:31.420][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 01:11:31.424][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.434][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 01:11:31.437][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.446][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 01:11:31.449][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.458][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 01:11:31.461][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 01:11:31.463][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 01:11:31.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.475][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 01:11:31.477][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 01:11:31.480][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.487][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[2024-06-27 01:11:31.489][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 01:11:31.492][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 01:11:31.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.502][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 01:11:31.504][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 01:11:31.507][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 01:11:31.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.516][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 01:11:31.519][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.529][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 01:11:31.532][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 01:11:31.535][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 01:11:31.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.544][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:31.547][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 01:11:31.550][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 01:11:31.553][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 01:11:31.556][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 01:11:31.559][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 01:11:31.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.569][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 01:11:31.572][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 01:11:31.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.582][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 01:11:31.585][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 01:11:31.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.596][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 01:11:31.599][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 01:11:31.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.607][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[2024-06-27 01:11:31.610][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 01:11:31.613][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 01:11:31.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.623][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 01:11:31.626][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 01:11:31.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.637][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:31.640][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 01:11:31.661][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 01:11:31.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.670][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 01:11:31.674][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 01:11:31.676][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 01:11:31.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:31.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:31.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:31.685][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 01:11:31.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.755][self$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[2024-06-27 01:11:31.758][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.761][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:31.763][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.767][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.775][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:31.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:31.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.782][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 01:11:31.784][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:31.786][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.789][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.791][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:31.791][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:31.791][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:31.791][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:31.791][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:31.794][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:31.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.801][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:31.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.807][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.809][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:31.814][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:31.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.820][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.824][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 01:11:31.828][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.830][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:31.833][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:31.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.842][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.847][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:31.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:31.852][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.854][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 01:11:31.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:31.859][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.863][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:31.863][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:31.863][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:31.863][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:31.863][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:31.866][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:31.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:31.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.882][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.884][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:31.886][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:31.888][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.891][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.894][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 01:11:31.898][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.900][self$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[2024-06-27 01:11:31.903][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:31.912][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.917][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:31.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:31.927][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.929][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 01:11:31.932][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:31.934][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.937][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.939][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.942][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:31.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.949][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:31.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:31.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:31.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.959][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:31.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:31.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.968][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:31.971][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 01:11:31.975][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.978][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:31.980][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.982][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:31.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:31.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:31.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:31.994][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:31.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:31.999][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:32.001][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 01:11:32.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:32.006][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:32.009][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.011][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:32.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:32.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:32.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:32.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:32.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:32.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:32.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:32.030][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:32.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:32.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:32.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:32.040][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:32.043][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:32.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.047][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[2024-06-27 01:11:32.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.062][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.DEBUG[2024-06-27 01:11:32.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.079][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.DEBUG[2024-06-27 01:11:32.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.237][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[2024-06-27 01:11:32.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.283][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 01:11:32.287][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 01:11:32.292][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 01:11:32.296][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 01:11:32.300][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:32.304][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 01:11:32.309][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:32.313][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:32.318][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 01:11:32.321][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 01:11:32.325][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:32.328][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 01:11:32.332][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:32.336][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:32.339][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 01:11:32.342][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 01:11:32.346][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 01:11:32.349][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 01:11:32.352][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:32.356][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 01:11:32.359][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 01:11:32.363][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 01:11:32.366][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 01:11:32.370][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 01:11:32.374][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 01:11:32.377][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 01:11:32.380][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 01:11:32.384][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 01:11:32.387][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 01:11:32.391][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 01:11:32.394][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 01:11:32.397][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 01:11:32.400][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 01:11:32.403][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 01:11:32.406][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 01:11:32.409][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 01:11:32.412][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 01:11:32.416][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 01:11:32.419][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 01:11:32.423][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 01:11:32.427][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 01:11:32.430][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 01:11:32.434][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 01:11:32.438][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 01:11:32.442][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 01:11:32.445][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 01:11:32.448][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 01:11:32.452][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 01:11:32.456][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 01:11:32.459][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 01:11:32.462][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 01:11:32.466][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 01:11:32.469][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 01:11:32.472][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 01:11:32.476][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 01:11:32.479][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 01:11:32.483][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 01:11:32.486][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 01:11:32.490][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 01:11:32.493][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 01:11:32.496][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 01:11:32.500][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 01:11:32.503][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 01:11:32.506][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 01:11:32.510][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 01:11:32.513][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 01:11:32.516][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:32.520][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:32.524][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 01:11:32.527][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 01:11:32.530][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 01:11:32.534][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 01:11:32.537][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 01:11:32.541][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 01:11:32.544][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 01:11:32.548][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 01:11:32.551][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 01:11:32.555][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 01:11:32.558][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 01:11:32.562][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 01:11:32.565][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 01:11:32.569][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 01:11:32.572][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 01:11:32.576][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 01:11:32.579][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:32.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:32.584][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.588][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:32.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:32.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:32.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:32.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:32.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:32.847][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:32.850][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-27 01:11:32.855][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:32.857][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 01:11:32.859][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.862][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:32.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:32.869][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.872][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-27 01:11:32.874][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-27 01:11:32.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:32.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.880][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-27 01:11:32.882][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-27 01:11:32.884][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-27 01:11:32.887][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:32.889][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:32.889][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:32.889][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:32.892][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-27 01:11:32.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:32.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:32.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:32.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:32.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:32.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:32.907][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:32.907][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-27 01:11:32.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:32.911][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:32.913][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:32.915][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-27 01:11:32.915][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-27 01:11:32.918][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:32.922][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:32.926][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-27 01:11:32.929][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:32.933][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:32.936][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:32.944][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-27 01:11:32.946][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-27 01:11:32.949][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-27 01:11:32.953][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-27 01:11:32.956][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:32.958][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:32.962][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-27 01:11:32.964][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-27 01:11:32.967][biodb::testThat]
biodb.INFO [2024-06-27 01:11:32.969][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-06-27 01:11:32.971][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:32.974][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:32.982][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-27 01:11:32.990][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:32.993][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-27 01:11:32.996][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:32.999][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-27 01:11:33.007][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.015][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-27 01:11:33.021][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.024][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-27 01:11:33.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.053][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.061][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.065][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-27 01:11:33.068][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.072][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-27 01:11:33.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.097][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[2024-06-27 01:11:33.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-27 01:11:33.189][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.192][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-27 01:11:33.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.231][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-27 01:11:33.238][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.241][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-27 01:11:33.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.291][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[2024-06-27 01:11:33.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.308][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.311][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-27 01:11:33.314][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.318][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-27 01:11:33.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.347][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.355][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.358][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-27 01:11:33.361][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.365][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-27 01:11:33.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:33.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:33.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-06-27 01:11:33.409][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:33.412][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-06-27 01:11:33.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:33.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:33.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:33.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:33.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:33.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:33.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 01:11:33.461][biodb::testThat]
biodb.INFO [2024-06-27 01:11:33.463][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-06-27 01:11:33.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:33.467][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:33.474][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:33.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:33.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:33.493][private$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[2024-06-27 01:11:33.908][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[2024-06-27 01:11:34.318][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:34.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-27 01:11:34.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-27 01:11:34.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:34.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:34.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:34.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:34.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:34.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:34.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:34.369][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[2024-06-27 01:11:34.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:34.380][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:34.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:11:34.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:11:35.240][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:35.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-27 01:11:35.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-27 01:11:35.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:35.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:35.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:35.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:35.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:35.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 01:11:35.292][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 01:11:35.294][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-27 01:11:35.297][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-27 01:11:35.299][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 01:11:35.301][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:35.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:35.305][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:35.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:35.309][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 01:11:35.319][biodb::testContext]
biodb.INFO [2024-06-27 01:11:35.321][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:35.323][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-27 01:11:35.325][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:35.327][biodb::testContext]
biodb.INFO [2024-06-27 01:11:35.332][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:35.336][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:35.344][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:35.346][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 01:11:35.348][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.354][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[2024-06-27 01:11:35.356][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 01:11:35.359][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.378][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 01:11:35.382][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.401][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 01:11:35.403][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 01:11:35.405][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 01:11:35.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.427][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 01:11:35.430][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 01:11:35.443][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.451][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 01:11:35.464][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 01:11:35.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.483][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 01:11:35.485][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 01:11:35.488][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 01:11:35.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.503][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.DEBUG[2024-06-27 01:11:35.506][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 01:11:35.508][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.526][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 01:11:35.529][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 01:11:35.542][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 01:11:35.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.563][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:35.565][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 01:11:35.568][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 01:11:35.570][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 01:11:35.583][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 01:11:35.586][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 01:11:35.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.604][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 01:11:35.607][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 01:11:35.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.623][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 01:11:35.626][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 01:11:35.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.644][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 01:11:35.647][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 01:11:35.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.669][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 01:11:35.685][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 01:11:35.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.709][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 01:11:35.713][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 01:11:35.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.738][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:35.741][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 01:11:35.786][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 01:11:35.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.794][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 01:11:35.808][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 01:11:35.813][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 01:11:35.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:35.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:35.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:35.835][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 01:11:35.850][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:35.853][self$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[2024-06-27 01:11:35.855][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:35.858][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:35.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:35.874][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:35.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:35.880][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:35.893][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:35.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:35.898][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:35.900][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 01:11:35.913][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:35.915][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:35.918][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:35.920][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:35.920][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:35.920][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:35.920][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:35.920][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:35.929][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:35.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:35.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:35.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:35.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:35.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:35.955][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:35.957][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:35.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:35.973][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:35.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:35.978][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:35.981][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 01:11:35.998][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.001][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:36.006][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:36.022][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.027][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.043][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.046][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:36.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:36.051][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.066][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 01:11:36.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:36.071][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.086][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:36.086][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:36.086][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:36.086][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:36.086][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:36.089][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:36.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:36.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.128][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:36.133][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:36.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.138][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.151][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 01:11:36.156][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.158][self$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[2024-06-27 01:11:36.171][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.173][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:36.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.178][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.195][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.197][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:36.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:36.215][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.218][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 01:11:36.221][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:36.223][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.238][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.242][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:36.247][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:36.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.270][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.284][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.287][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:36.289][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:36.292][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.307][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.310][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 01:11:36.314][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.325][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:36.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:36.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.347][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.351][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.355][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:36.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:36.369][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.372][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 01:11:36.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:36.388][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:36.395][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:36.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:36.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:36.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:36.434][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:36.436][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.438][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:36.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:36.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:36.457][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:36.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:36.473][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:36.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:36.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:36.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:36.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:36.967][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 01:11:36.971][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 01:11:36.985][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 01:11:36.989][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 01:11:36.992][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:37.007][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 01:11:37.011][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:37.025][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:37.028][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 01:11:37.032][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 01:11:37.046][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:37.049][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 01:11:37.052][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:37.067][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:37.071][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 01:11:37.074][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 01:11:37.087][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 01:11:37.091][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 01:11:37.094][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:37.109][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 01:11:37.113][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 01:11:37.116][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 01:11:37.130][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 01:11:37.133][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 01:11:37.147][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 01:11:37.151][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 01:11:37.155][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 01:11:37.168][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 01:11:37.171][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 01:11:37.176][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 01:11:37.189][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 01:11:37.192][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 01:11:37.196][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 01:11:37.208][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 01:11:37.212][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 01:11:37.224][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 01:11:37.228][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 01:11:37.231][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 01:11:37.247][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 01:11:37.254][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 01:11:37.258][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 01:11:37.272][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 01:11:37.275][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 01:11:37.279][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 01:11:37.291][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 01:11:37.295][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 01:11:37.312][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 01:11:37.317][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 01:11:37.322][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 01:11:37.342][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 01:11:37.345][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 01:11:37.349][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 01:11:37.358][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 01:11:37.361][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 01:11:37.373][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 01:11:37.377][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 01:11:37.380][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 01:11:37.392][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 01:11:37.396][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 01:11:37.399][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 01:11:37.417][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 01:11:37.420][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 01:11:37.435][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 01:11:37.439][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 01:11:37.442][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 01:11:37.457][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 01:11:37.461][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:37.466][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:37.477][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 01:11:37.481][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 01:11:37.492][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 01:11:37.502][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 01:11:37.505][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 01:11:37.518][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 01:11:37.521][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 01:11:37.525][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 01:11:37.536][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 01:11:37.540][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 01:11:37.544][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 01:11:37.558][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 01:11:37.562][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 01:11:37.565][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 01:11:37.581][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 01:11:37.584][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 01:11:37.588][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:37.602][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:37.604][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.608][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.798][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[2024-06-27 01:11:37.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:37.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.972][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.DEBUG[2024-06-27 01:11:37.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:37.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:37.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:37.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:37.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:37.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:37.999][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.DEBUG[2024-06-27 01:11:38.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:38.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:38.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:38.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:38.036][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.DEBUG[2024-06-27 01:11:38.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:38.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:38.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:38.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:38.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:38.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:38.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:38.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:38.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:38.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:38.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:38.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:38.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:38.097][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.DEBUG[2024-06-27 01:11:38.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:38.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:38.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:38.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:38.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:38.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:38.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:38.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:38.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:38.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:38.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:38.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:38.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:38.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:38.175][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:38.178][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-27 01:11:38.183][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:38.197][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 01:11:38.199][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:38.202][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:38.204][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:38.218][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:38.221][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:38.223][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-27 01:11:38.225][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-27 01:11:38.237][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:38.240][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:38.242][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-27 01:11:38.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-27 01:11:38.247][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-27 01:11:38.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:38.264][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:38.264][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:38.264][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:38.267][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-27 01:11:38.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:38.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:38.285][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:38.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:38.300][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:38.302][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:38.305][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:38.305][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-27 01:11:38.307][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:38.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:38.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:38.344][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-27 01:11:38.344][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-27 01:11:38.347][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:38.359][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:38.363][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-27 01:11:38.366][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:38.385][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:38.389][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:38.409][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-27 01:11:38.411][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-27 01:11:38.414][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-27 01:11:38.429][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-27 01:11:38.432][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:38.435][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:38.449][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-27 01:11:38.451][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-27 01:11:38.454][biodb::testThat]
biodb.INFO [2024-06-27 01:11:38.457][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-27 01:11:38.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:38.474][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:38.491][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-27 01:11:38.500][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 01:11:38.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-27 01:11:38.507][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 01:11:38.525][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-27 01:11:38.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-27 01:11:38.555][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:38.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:38.572][private$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[2024-06-27 01:11:39.099][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[2024-06-27 01:11:39.512][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:39.516][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-27 01:11:39.526][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-27 01:11:39.544][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 01:11:39.546][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-27 01:11:39.549][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-27 01:11:39.551][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 01:11:39.553][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:39.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:39.557][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:39.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:39.560][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.562][FUN] Functions in observer BiodbConfig: [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 [2024-06-27 01:11:39.570][biodb::testContext]
biodb.INFO [2024-06-27 01:11:39.572][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:39.575][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-27 01:11:39.577][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 01:11:39.579][biodb::testContext]
biodb.INFO [2024-06-27 01:11:39.584][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:39.587][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:39.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:39.598][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 01:11:39.600][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.609][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 01:11:39.611][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.619][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 01:11:39.622][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.641][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 01:11:39.643][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 01:11:39.647][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 01:11:39.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.666][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 01:11:39.669][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 01:11:39.671][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.690][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 01:11:39.703][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 01:11:39.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.713][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 01:11:39.725][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 01:11:39.728][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 01:11:39.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.788][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 01:11:39.790][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.808][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 01:11:39.810][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 01:11:39.823][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 01:11:39.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.832][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:39.845][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 01:11:39.848][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 01:11:39.851][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 01:11:39.858][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 01:11:39.861][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 01:11:39.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.880][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 01:11:39.882][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 01:11:39.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.902][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 01:11:39.904][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 01:11:39.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.922][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 01:11:39.925][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 01:11:39.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.945][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 01:11:39.958][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 01:11:39.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.978][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 01:11:39.981][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 01:11:39.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:39.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:39.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:39.999][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 01:11:40.001][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 01:11:40.024][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 01:11:40.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.037][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 01:11:40.040][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 01:11:40.043][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 01:11:40.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.059][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 01:11:40.063][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.075][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-27 01:11:40.077][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:40.081][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.094][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.096][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.098][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.101][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:40.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:40.118][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.120][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 01:11:40.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:40.136][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.138][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:40.141][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:40.141][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:40.141][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:40.141][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:40.143][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:40.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:40.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.177][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.180][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:40.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:40.198][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.201][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.204][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 01:11:40.218][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.221][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:40.223][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:40.238][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.243][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.258][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:40.261][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:40.263][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.265][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 01:11:40.281][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:40.284][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.287][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.289][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:40.289][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:40.289][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:40.289][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 01:11:40.289][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 01:11:40.305][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:40.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:40.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.329][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.331][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:40.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:40.348][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.350][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.353][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 01:11:40.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.369][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-27 01:11:40.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:40.386][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.388][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.390][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.406][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 01:11:40.409][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:40.412][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.414][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 01:11:40.426][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:40.429][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.431][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.434][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.447][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:40.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:40.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.474][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:40.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:40.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.496][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.509][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 01:11:40.513][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.516][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 01:11:40.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:40.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.539][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 01:11:40.577][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:40.580][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.583][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 01:11:40.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:40.599][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.601][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:40.605][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 01:11:40.622][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.640][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:40.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:40.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:40.648][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:40.661][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.664][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:40.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:40.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:40.679][self$setPropertyValue]
biodb.DEBUG[2024-06-27 01:11:40.683][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:40.685][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.786][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[2024-06-27 01:11:40.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.915][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.DEBUG[2024-06-27 01:11:40.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:40.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:40.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:40.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:40.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:40.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.008][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[2024-06-27 01:11:41.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.092][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[2024-06-27 01:11:41.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.179][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[2024-06-27 01:11:41.182][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 01:11:41.197][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 01:11:41.201][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 01:11:41.217][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 01:11:41.221][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:41.226][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 01:11:41.245][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:41.249][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:41.264][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 01:11:41.268][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 01:11:41.272][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:41.283][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 01:11:41.287][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 01:11:41.290][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 01:11:41.304][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 01:11:41.308][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 01:11:41.320][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 01:11:41.324][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 01:11:41.328][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:41.342][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 01:11:41.345][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 01:11:41.377][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 01:11:41.381][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 01:11:41.384][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 01:11:41.396][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 01:11:41.399][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 01:11:41.408][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 01:11:41.412][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 01:11:41.415][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 01:11:41.418][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 01:11:41.433][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 01:11:41.436][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 01:11:41.439][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 01:11:41.455][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 01:11:41.458][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 01:11:41.476][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 01:11:41.480][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 01:11:41.486][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 01:11:41.491][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 01:11:41.495][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 01:11:41.511][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 01:11:41.515][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 01:11:41.518][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 01:11:41.531][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 01:11:41.534][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 01:11:41.537][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 01:11:41.553][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 01:11:41.556][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 01:11:41.570][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 01:11:41.574][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 01:11:41.578][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 01:11:41.596][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 01:11:41.599][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 01:11:41.603][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 01:11:41.617][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 01:11:41.621][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 01:11:41.624][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 01:11:41.639][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 01:11:41.642][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 01:11:41.645][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 01:11:41.660][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 01:11:41.664][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 01:11:41.679][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 01:11:41.685][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 01:11:41.689][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 01:11:41.704][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 01:11:41.708][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:41.722][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:41.725][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 01:11:41.744][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 01:11:41.751][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 01:11:41.754][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 01:11:41.770][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 01:11:41.774][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 01:11:41.778][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 01:11:41.793][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 01:11:41.796][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 01:11:41.811][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 01:11:41.815][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 01:11:41.819][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 01:11:41.832][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 01:11:41.838][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 01:11:41.841][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 01:11:41.856][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 01:11:41.860][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 01:11:41.862][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 01:11:41.876][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.881][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:41.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:41.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:41.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:41.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:41.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:41.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:41.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:41.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:41.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:41.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:41.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:41.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.013][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.DEBUG[2024-06-27 01:11:42.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.049][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[2024-06-27 01:11:42.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.090][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[2024-06-27 01:11:42.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.351][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[2024-06-27 01:11:42.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.371][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[2024-06-27 01:11:42.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.437][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[2024-06-27 01:11:42.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 01:11:42.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:42.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:42.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:42.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:42.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:42.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:42.481][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-27 01:11:42.498][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-27 01:11:42.503][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:42.505][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 01:11:42.520][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:42.523][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 01:11:42.525][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:42.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 01:11:42.544][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:42.547][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-27 01:11:42.549][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-27 01:11:42.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 01:11:42.567][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:42.569][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-27 01:11:42.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-27 01:11:42.574][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-27 01:11:42.594][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 01:11:42.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 01:11:42.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 01:11:42.596][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 01:11:42.599][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-27 01:11:42.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:42.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:42.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 01:11:42.618][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 01:11:42.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 01:11:42.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 01:11:42.636][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:42.636][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-27 01:11:42.638][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 01:11:42.640][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 01:11:42.655][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 01:11:42.657][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-27 01:11:42.657][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-27 01:11:42.661][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 01:11:42.675][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 01:11:42.679][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-27 01:11:42.683][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 01:11:42.696][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 01:11:42.700][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 01:11:42.718][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-27 01:11:42.742][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-27 01:11:42.756][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-27 01:11:42.760][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-27 01:11:42.763][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:42.776][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-27 01:11:42.779][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-27 01:11:42.781][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-27 01:11:42.784][biodb::testThat]
biodb.INFO [2024-06-27 01:11:42.795][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-27 01:11:42.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 01:11:42.799][biodb::testThat]
biodb.DEBUG[2024-06-27 01:11:42.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.INFO [2024-06-27 01:11:42.834][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-06-27 01:11:42.838][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:42.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:42.844][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-27 01:11:43.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-27 01:11:43.792][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:43.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-27 01:11:43.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-27 01:11:43.814][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[2024-06-27 01:11:43.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:43.824][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:43.828][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-27 01:11:44.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-27 01:11:44.644][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:44.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-27 01:11:44.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.DEBUG[2024-06-27 01:11:44.667][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-27 01:11:44.670][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 01:11:44.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-27 01:11:44.676][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 01:11:44.679][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 01:11:44.681][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 01:11:44.683][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-27 01:11:44.686][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 01:11:44.688][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 01:11:44.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:44.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:44.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:44.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:44.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:44.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:44.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 01:11:44.718][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-27 01:11:44.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 01:11:44.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 01:11:44.739][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-27 01:11:45.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-27 01:11:45.936][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 01:11:45.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-27 01:11:45.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-27 01:11:45.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-27 01:11:45.963][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 01:11:45.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-27 01:11:45.969][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-27 01:11:45.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 01:11:45.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:45.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:45.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:45.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:45.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:45.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 01:11:46.007][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.010][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.029][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:46.031][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:46.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.037][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-27 01:11:46.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-27 01:11:46.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.051][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:46.054][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:46.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 01:11:46.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 01:11:46.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-27 01:11:46.074][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-27 01:11:46.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.085][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.088][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-27 01:11:46.090][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-27 01:11:46.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.106][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.109][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:46.124][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:46.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.128][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:46.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 01:11:46.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.153][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:46.166][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:46.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.171][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.174][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-27 01:11:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 01:11:46.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:46.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:46.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:46.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 01:11:46.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.244][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:46.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:46.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.261][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 01:11:46.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 01:11:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.299][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:46.301][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:46.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.321][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-27 01:11:46.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-27 01:11:46.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.343][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:46.346][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:46.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.364][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-27 01:11:46.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-27 01:11:46.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 01:11:46.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 01:11:46.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 01:11:46.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 01:11:46.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 01:11:46.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 01:11:46.650][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-27 01:11:46.670][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 01:11:46.673][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-27 01:11:46.676][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-27 01:11:46.690][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 01:11:46.692][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 01:11:46.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 01:11:46.698][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 01:11:46.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 01:11:46.714][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 01:11:46.717][FUN] Functions in observer 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 385 ]
>
> proc.time()
user system elapsed
41.615 1.987 85.245
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.948 | 2.353 | 10.683 | |
| ChebiEntry | 0.851 | 0.024 | 0.902 | |