Pierrick Roger
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_14 |
| git_last_commit: 35326c0 |
| git_last_commit_date: 2021-10-27 06:00:18 -0400 (Wed, 27 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:41 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the biodbChebi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/biodbChebi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 176/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.0.1 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodbChebi |
| Version: 1.0.1 |
| 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_1.0.1.tar.gz |
| StartedAt: 2022-04-12 10:51:29 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 10:54:06 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 157.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbChebi.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 4.335 0.626 5.95
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2022-04-12 10:52:39.443][biodb::testContext]
biodb.INFO [2022-04-12 10:52:39.459][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:39.461][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-04-12 10:52:39.464][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:52:39.466][biodb::testContext]
biodb.INFO [2022-04-12 10:52:39.508][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:52:39.511][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:52:39.524][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:39.526][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:52:39.527][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.535][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:52:39.583][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.590][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[2022-04-12 10:52:39.592][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:52:39.595][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.601][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:52:39.603][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:52:39.605][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:52:39.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.610][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[2022-04-12 10:52:39.613][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:52:39.615][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:52:39.617][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.626][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:52:39.628][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:52:39.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.637][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:52:39.640][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:52:39.643][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:52:39.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.651][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:52:39.654][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.663][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:52:39.665][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:52:39.668][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:52:39.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.676][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:39.678][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:52:39.681][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:52:39.683][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:52:39.685][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:52:39.688][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:52:39.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.696][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:52:39.697][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:52:39.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.706][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:52:39.708][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:52:39.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.715][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[2022-04-12 10:52:39.717][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:52:39.719][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:52:39.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.727][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:52:39.729][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:52:39.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.735][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:52:39.738][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:52:39.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.746][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:52:39.749][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:52:39.760][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:52:39.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.769][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:52:39.771][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:52:39.773][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:52:39.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:39.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:39.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:39.786][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:52:39.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:39.907][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:52:39.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.911][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:39.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.916][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:39.917][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:39.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:39.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:39.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:39.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.928][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:52:39.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:39.931][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:39.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.945][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:39.945][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:39.945][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:39.945][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:39.945][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:39.947][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:39.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:39.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:39.952][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:39.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:39.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:39.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:39.958][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:39.959][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:39.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:39.962][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:39.964][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:39.966][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:52:39.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:39.971][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:39.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:39.976][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:39.979][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:39.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:39.982][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:39.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:39.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.987][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:52:39.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:39.991][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:39.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:39.994][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:39.994][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:39.994][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:39.994][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:52:39.994][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:52:39.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:39.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:39.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:40.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.007][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.009][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:40.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:40.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.015][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.018][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:52:40.021][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.023][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:52:40.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.027][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:40.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.034][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.038][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:52:40.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:40.040][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.041][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:52:40.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:40.044][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.048][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.050][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:40.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:40.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.063][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.065][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:40.066][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:40.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.069][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.071][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:52:40.075][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.078][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:52:40.080][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:40.084][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.088][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.091][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:52:40.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:40.094][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.096][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:52:40.098][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:40.100][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.102][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.103][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.105][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:52:40.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:40.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.116][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.118][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:40.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:40.122][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.124][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:52:40.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:40.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.157][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[2022-04-12 10:52:40.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.172][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[2022-04-12 10:52:40.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.288][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:52:40.298][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:52:40.301][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:52:40.304][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:52:40.307][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:52:40.310][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:52:40.314][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:52:40.317][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:52:40.320][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:52:40.324][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:52:40.327][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:52:40.330][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:52:40.333][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:52:40.336][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:52:40.339][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:52:40.342][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:52:40.344][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:52:40.347][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:52:40.350][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:52:40.353][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:52:40.356][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:52:40.360][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:52:40.363][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:52:40.366][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:52:40.370][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:52:40.373][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:52:40.376][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:52:40.380][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:52:40.383][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:52:40.386][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:52:40.389][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:52:40.391][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:52:40.394][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:52:40.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:52:40.398][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:52:40.400][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:52:40.403][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:52:40.406][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:52:40.409][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:52:40.412][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:52:40.414][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:52:40.418][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:52:40.421][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:52:40.425][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:52:40.429][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:52:40.432][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:52:40.435][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:52:40.438][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:52:40.449][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:52:40.452][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:52:40.455][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:52:40.458][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:52:40.460][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:52:40.463][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:52:40.467][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:52:40.469][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:52:40.473][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:52:40.476][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:52:40.478][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:52:40.482][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:52:40.484][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:52:40.487][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:52:40.489][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:52:40.492][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:52:40.496][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:52:40.500][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:52:40.503][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:52:40.505][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:52:40.508][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:52:40.511][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:52:40.513][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:52:40.516][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:52:40.518][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:52:40.521][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:52:40.524][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:52:40.528][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:52:40.531][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:52:40.534][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:52:40.536][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:52:40.539][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:52:40.542][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:52:40.544][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:52:40.547][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:52:40.559][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:52:40.561][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:52:40.568][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:52:40.570][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.574][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.575][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.DEBUG[2022-04-12 10:52:40.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.597][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.DEBUG[2022-04-12 10:52:40.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.621][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[2022-04-12 10:52:40.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.634][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[2022-04-12 10:52:40.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.647][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[2022-04-12 10:52:40.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.683][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[2022-04-12 10:52:40.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.709][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.DEBUG[2022-04-12 10:52:40.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.764][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[2022-04-12 10:52:40.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:40.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:52:40.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:40.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:40.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:40.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:40.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:40.788][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[2022-04-12 10:52:40.791][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 10:52:40.811][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 10:52:40.815][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.817][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.819][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:52:40.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.824][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.826][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.829][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 10:52:40.831][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:52:40.833][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:52:40.835][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.836][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 10:52:40.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 10:52:40.841][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 10:52:40.844][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:52:40.846][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:52:40.846][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:52:40.846][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:52:40.849][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:52:40.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.853][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.855][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:52:40.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:52:40.858][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:52:40.859][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:52:40.861][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:52:40.861][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 10:52:40.863][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:52:40.865][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:52:40.867][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:52:40.869][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 10:52:40.869][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 10:52:40.880][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:52:40.882][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:52:40.885][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 10:52:40.887][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:52:40.890][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:52:40.893][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:52:40.940][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 10:52:40.942][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 10:52:40.951][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 10:52:40.967][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 10:52:40.976][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:40.978][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:52:40.981][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 10:52:40.983][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 10:52:41.049][biodb::testThat]
biodb.INFO [2022-04-12 10:52:41.050][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2022-04-12 10:52:41.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:41.053][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:41.059][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2022-04-12 10:52:41.076][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:41.083][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:52:41.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:41.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:41.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:41.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:41.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:41.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:41.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:41.129][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.133][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.135][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.187][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:41.189][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:41.191][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.193][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.269][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:41.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:41.273][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.275][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.278][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:41.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:41.306][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.308][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.338][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.340][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.342][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.343][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.370][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:41.373][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:41.375][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.377][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.378][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:41.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.402][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:41.405][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.407][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.409][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:41.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.449][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:41.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:41.452][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.454][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.482][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:41.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:41.486][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.488][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.515][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:41.517][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:41.519][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.520][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.522][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.547][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:41.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:41.550][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.552][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:41.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:41.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:41.744][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2022-04-12 10:52:41.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:41.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:41.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:41.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.829][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:41.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:41.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.866][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:41.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:41.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:41.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.881][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:41.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:41.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:41.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:41.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:41.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:41.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:41.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:41.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.091][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.093][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.097][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.147][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.149][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:42.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:42.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:42.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:42.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:42.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.195][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:42.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:42.200][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.201][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:42.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:42.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.239][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.246][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.248][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.250][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.252][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.325][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.326][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.327][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.329][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:42.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.376][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.378][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.380][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:42.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.410][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.425][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.427][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.429][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.431][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.432][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.452][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.476][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.478][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.480][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.482][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:42.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.504][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.521][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.529][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.532][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.534][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.536][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:42.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:42.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:42.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:42.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:42.583][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:42.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.587][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:42.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.635][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.636][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.638][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.641][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:42.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.681][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.683][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.684][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.686][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.709][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:42.711][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:42.713][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.715][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.732][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:42.931][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:42.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.959][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.979][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:42.981][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:42.983][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:42.984][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:42.994][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:42.996][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:42.998][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.000][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.013][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.015][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.024][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.026][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.028][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.030][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.039][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:43.041][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:43.042][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.044][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.053][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.055][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.057][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.058][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.069][ef$get] Asked field names are: n.stars.
biodb.TRACE[2022-04-12 10:52:43.071][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:43.073][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.076][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.085][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.087][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.089][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.090][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.099][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:43.102][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:43.104][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.105][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:43.115][biodb::testThat]
biodb.INFO [2022-04-12 10:52:43.117][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-04-12 10:52:43.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:43.121][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:43.152][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2022-04-12 10:52:43.166][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:52:43.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2022-04-12 10:52:43.174][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:43.177][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2022-04-12 10:52:43.179][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:43.284][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:43.286][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:52:43.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:43.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:43.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:43.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:43.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:43.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:43.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:43.304][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.309][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.310][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.381][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:43.383][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:43.385][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.387][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.389][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:43.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:43.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.414][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:43.416][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:43.418][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.420][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.423][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:43.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:43.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.449][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:43.452][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:43.454][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.456][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:43.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:43.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.484][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.487][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.489][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.491][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:43.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.515][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.520][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.522][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.549][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:43.551][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:43.553][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.555][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:43.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.584][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.586][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.588][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:43.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.616][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.620][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.622][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.648][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:43.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:43.652][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.653][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:43.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.685][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:43.687][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:43.689][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.691][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.693][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:43.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:43.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:43.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:43.831][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2022-04-12 10:52:43.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-04-12 10:52:43.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-04-12 10:52:43.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:52:43.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-04-12 10:52:43.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:52:43.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-04-12 10:52:43.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:43.870][biodb::testThat]
biodb.INFO [2022-04-12 10:52:43.872][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2022-04-12 10:52:43.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:43.875][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:43.881][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.884][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.886][ef$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:43.889][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2022-04-12 10:52:43.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:43.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:43.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:43.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:43.973][function(conn, opt)] With value "squalene".
biodb.DEBUG[2022-04-12 10:52:44.000][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 10:52:44.039][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:52:44.077][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 10:52:44.080][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:44.083][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 10:52:44.136][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[2022-04-12 10:52:44.142][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:44.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:44.147][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:52:45.066][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:52:45.852][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:45.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2022-04-12 10:52:45.969][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2022-04-12 10:52:45.991][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2022-04-12 10:52:46.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:46.018][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:46.019][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.021][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.023][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.026][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.028][ef$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:46.032][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.034][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2022-04-12 10:52:46.036][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:46.038][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:46.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:46.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:46.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:46.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:46.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:46.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:46.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:46.228][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:52:46.233][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:52:46.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:52:46.238][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:46.240][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2022-04-12 10:52:46.268][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.269][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2022-04-12 10:52:46.271][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:46.273][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:46.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:46.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:46.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:46.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:46.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:46.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:46.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:46.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:46.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:46.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.906][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-04-12 10:52:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.914][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:46.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-04-12 10:52:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:46.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:46.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-04-12 10:52:46.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:46.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:52:46.934][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.936][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-04-12 10:52:46.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:46.939][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.948][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.949][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-04-12 10:52:46.951][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:46.953][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.963][biodb::testThat]
biodb.INFO [2022-04-12 10:52:46.965][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2022-04-12 10:52:46.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:46.969][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:46.976][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2022-04-12 10:52:47.759][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2022-04-12 10:52:48.996][biodb::testThat]
biodb.INFO [2022-04-12 10:52:48.998][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2022-04-12 10:52:49.000][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:49.002][biodb::testThat]
biodb.DEBUG[2022-04-12 10:52:49.699][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.INFO [2022-04-12 10:52:50.218][biodb::testThat]
biodb.INFO [2022-04-12 10:52:50.220][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2022-04-12 10:52:50.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:52:50.224][biodb::testThat]
biodb.TRACE[2022-04-12 10:52:50.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:50.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:50.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:50.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:50.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:50.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:50.367][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:52:50.374][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:52:50.377][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:52:50.380][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:50.383][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 10:52:50.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:52:50.413][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:52:50.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:52:50.418][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:50.420][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2022-04-12 10:52:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:52:50.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:50.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:50.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:50.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:50.570][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:52:50.602][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:50.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:50.638][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:52:51.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:52:51.784][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:51.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content"
biodb.TRACE[2022-04-12 10:52:51.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.request"
biodb.DEBUG[2022-04-12 10:52:51.840][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[2022-04-12 10:52:51.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:51.847][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:51.850][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:52:52.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:52:53.129][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:53.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content"
biodb.TRACE[2022-04-12 10:52:53.172][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.request"
biodb.DEBUG[2022-04-12 10:52:53.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:53.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:53.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:53.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:53.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:53.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:53.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:53.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:53.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:53.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:53.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:53.272][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:52:53.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:53.280][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:53.283][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:52:53.988][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:52:55.799][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:55.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content"
biodb.TRACE[2022-04-12 10:52:55.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.request"
biodb.DEBUG[2022-04-12 10:52:55.892][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[2022-04-12 10:52:55.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:52:55.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:52:55.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:52:55.903][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 10:52:55.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:55.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:55.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:55.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:55.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:55.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:55.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:55.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:55.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:55.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:55.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:55.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:55.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:55.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:55.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:55.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:56.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:56.002][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[2022-04-12 10:52:56.003][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2022-04-12 10:52:56.088][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:52:56.091][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2022-04-12 10:52:56.094][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:52:56.096][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:52:56.097][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:56.099][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:52:56.101][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:52:56.103][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:52:56.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:56.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:56.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:56.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:56.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:56.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:56.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:56.119][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2022-04-12 10:52:56.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:56.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:56.130][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2022-04-12 10:52:56.664][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2022-04-12 10:52:57.193][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:57.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2022-04-12 10:52:57.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2022-04-12 10:52:57.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2022-04-12 10:52:57.291][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:52:57.321][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:57.323][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:52:57.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:57.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:57.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:57.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:57.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:57.337][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:57.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:57.343][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.345][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.347][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.349][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.368][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:57.370][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:57.372][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.374][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.376][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:57.378][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:57.380][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.381][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.383][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:57.384][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:57.386][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.388][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.390][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:57.392][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:57.394][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.396][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.399][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:57.401][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:57.403][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.405][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.407][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:57.410][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.411][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.414][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.419][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:57.421][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.423][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.426][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.428][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.430][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.432][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:57.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.450][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:57.451][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:57.452][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.453][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.455][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:57.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.467][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:57.469][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:57.470][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.472][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:57.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:57.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:57.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.535][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2022-04-12 10:52:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:57.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:57.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:57.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:57.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:57.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:57.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:57.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:57.589][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2022-04-12 10:52:57.590][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:52:57.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2022-04-12 10:52:57.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:52:57.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:52:57.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:57.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:52:57.600][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:52:57.602][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:52:57.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:57.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:57.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:57.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:57.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:57.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:57.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:57.646][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2022-04-12 10:52:57.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:57.651][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:57.653][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2022-04-12 10:52:58.150][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2022-04-12 10:52:58.788][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:52:58.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2022-04-12 10:52:58.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2022-04-12 10:52:58.858][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2022-04-12 10:52:58.867][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:52:58.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:52:58.924][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:52:58.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:58.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:58.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:58.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:58.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:58.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:58.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:52:58.945][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.951][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:58.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:58.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.969][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:52:58.972][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:52:58.973][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.975][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.978][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:52:58.980][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:52:58.982][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.984][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.986][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:52:58.989][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:52:58.991][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:58.993][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:58.995][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:52:58.997][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:52:58.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.001][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.003][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:59.005][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:52:59.007][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.009][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.011][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:52:59.013][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.015][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.016][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.019][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:59.020][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:52:59.021][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.022][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.024][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:59.025][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:59.027][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.029][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:52:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:52:59.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.047][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:59.049][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:59.051][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.053][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.055][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:52:59.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:52:59.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.071][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:52:59.073][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:52:59.075][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.077][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:52:59.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:52:59.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:52:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:59.152][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2022-04-12 10:52:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:52:59.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:52:59.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:52:59.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:52:59.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:59.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:59.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:59.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.205][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2022-04-12 10:52:59.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:52:59.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2022-04-12 10:52:59.210][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:52:59.211][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:52:59.212][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:52:59.213][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:52:59.215][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:52:59.216][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:52:59.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:52:59.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:52:59.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:52:59.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:52:59.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:52:59.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:52:59.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:52:59.236][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2022-04-12 10:52:59.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:52:59.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:52:59.245][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2022-04-12 10:52:59.750][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2022-04-12 10:53:00.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:00.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2022-04-12 10:53:00.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2022-04-12 10:53:00.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2022-04-12 10:53:00.350][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:00.377][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:00.380][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:00.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:00.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:00.397][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.400][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.402][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.416][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:00.418][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:00.419][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.421][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.423][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:00.425][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:00.427][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.429][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.431][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:00.434][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:00.436][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.437][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:00.441][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:00.443][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.445][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.447][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:00.450][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.452][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.454][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:00.456][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.457][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.458][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.460][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:00.462][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:00.464][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.466][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.468][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:00.470][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:00.472][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.474][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:00.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:00.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.501][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:00.504][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:00.505][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.508][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:00.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.523][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:00.525][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:00.527][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.529][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:00.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:00.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:00.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:00.620][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2022-04-12 10:53:00.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:00.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:00.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:00.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:00.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:00.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:00.675][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2022-04-12 10:53:00.677][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:00.680][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2022-04-12 10:53:00.683][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:00.685][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:00.687][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:00.689][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:00.690][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:00.692][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:00.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:00.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:00.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:00.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:00.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:00.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:00.707][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[2022-04-12 10:53:00.708][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2022-04-12 10:53:00.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:00.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:00.719][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2022-04-12 10:53:01.223][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2022-04-12 10:53:01.752][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:01.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2022-04-12 10:53:01.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2022-04-12 10:53:01.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2022-04-12 10:53:01.840][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:01.873][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:01.875][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:01.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:01.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:01.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:01.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:01.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:01.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:01.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:01.891][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.896][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.897][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:01.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:01.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.915][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:01.918][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:01.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.921][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.923][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:01.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.937][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.939][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.940][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.942][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:01.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:01.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.958][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.962][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.964][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:01.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:01.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.982][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.985][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.986][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.988][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:01.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:01.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:01.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.006][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:02.008][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:02.010][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.012][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:02.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:02.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.025][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:02.027][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.029][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.031][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:02.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.044][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:02.046][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:02.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.050][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:02.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:02.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.066][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:02.068][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:02.070][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.072][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.088][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:02.090][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:02.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.092][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.093][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:02.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:02.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.114][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:02.116][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:02.118][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.120][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.122][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:02.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:02.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:02.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:02.197][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2022-04-12 10:53:02.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:02.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:02.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:02.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:02.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:02.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:02.229][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2022-04-12 10:53:02.231][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:02.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2022-04-12 10:53:02.237][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:02.239][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:02.241][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:02.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:02.245][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:02.247][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:02.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:02.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:02.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:02.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:02.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:02.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:02.262][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[2022-04-12 10:53:02.264][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2022-04-12 10:53:02.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:02.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:02.271][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2022-04-12 10:53:02.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2022-04-12 10:53:03.278][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:03.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2022-04-12 10:53:03.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2022-04-12 10:53:03.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2022-04-12 10:53:03.377][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:03.417][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:03.419][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:03.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:03.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:03.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:03.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:03.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:03.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:03.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:03.440][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.442][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.444][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.446][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.465][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:03.467][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:03.469][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.471][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.474][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:03.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:03.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.487][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.489][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.490][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.492][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.495][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:03.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:03.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.511][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.513][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.515][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.517][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:03.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:03.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.534][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.537][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.539][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:03.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.557][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.559][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.561][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.563][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.565][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:03.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.580][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:03.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.584][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.585][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.587][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:03.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.605][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.607][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.609][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:03.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.627][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:03.628][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:03.630][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.631][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:03.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:03.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.649][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:03.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:03.652][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.654][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.656][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:03.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:03.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.672][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:03.674][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:03.676][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.677][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:03.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:03.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:03.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:03.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:03.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:03.783][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2022-04-12 10:53:03.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:03.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:03.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:03.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:03.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:03.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:03.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:03.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:03.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:03.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:03.820][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2022-04-12 10:53:03.822][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:03.825][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2022-04-12 10:53:03.828][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:03.830][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:03.832][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:03.834][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:03.836][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:03.838][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:03.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:03.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:03.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:03.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:03.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:03.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:03.854][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[2022-04-12 10:53:03.856][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2022-04-12 10:53:03.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:03.863][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:03.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2022-04-12 10:53:04.360][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2022-04-12 10:53:04.871][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:04.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2022-04-12 10:53:04.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2022-04-12 10:53:04.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2022-04-12 10:53:04.989][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:05.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:05.030][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:05.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:05.052][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.055][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.058][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.060][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.075][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:05.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:05.078][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.079][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.081][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:05.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:05.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.095][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:05.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:05.099][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.101][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:05.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:05.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.119][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:05.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:05.123][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.125][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:05.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:05.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.145][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.147][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.149][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:05.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.166][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:05.168][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.170][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.173][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:05.176][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.178][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.180][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.183][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:05.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.201][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.202][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:05.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.219][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.221][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.223][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.225][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:05.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.244][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:05.246][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:05.249][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.251][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:05.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:05.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.270][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:05.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:05.275][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.278][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:05.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:05.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:05.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:05.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.401][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2022-04-12 10:53:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:05.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:05.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:05.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.432][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[2022-04-12 10:53:05.433][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2022-04-12 10:53:05.434][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:05.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2022-04-12 10:53:05.440][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:05.442][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:05.444][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:05.446][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:05.447][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:05.448][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:05.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:05.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:05.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:05.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:05.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:05.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:05.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:05.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2022-04-12 10:53:05.465][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:05.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:05.470][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2022-04-12 10:53:05.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2022-04-12 10:53:06.501][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:06.518][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2022-04-12 10:53:06.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2022-04-12 10:53:06.891][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2022-04-12 10:53:06.901][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:06.937][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:06.953][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:06.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:06.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:06.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:06.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:06.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:06.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:06.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:06.975][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:06.977][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:06.979][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.980][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:06.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:06.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:06.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:06.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:06.996][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:06.998][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:07.000][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.002][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:07.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:07.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.020][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:07.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:07.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.026][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:07.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:07.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.043][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:07.046][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:07.048][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.049][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:07.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:07.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:07.069][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:07.071][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.073][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:07.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.092][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:07.094][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:07.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.096][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.097][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:07.099][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.101][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.103][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.105][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:07.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.118][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:07.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:07.122][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.124][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:07.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.143][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:07.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:07.147][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.149][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:07.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:07.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.168][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:07.171][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:07.172][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.174][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.176][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:07.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.189][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:07.191][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:07.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.194][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.197][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:07.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:07.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:07.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:07.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:07.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:07.301][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2022-04-12 10:53:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:07.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:07.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:07.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:07.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:07.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:07.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:07.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:07.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:07.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:07.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:07.342][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2022-04-12 10:53:07.344][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:07.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2022-04-12 10:53:07.349][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:07.351][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:07.353][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:07.355][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:07.358][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:07.360][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:07.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:07.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:07.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:07.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:07.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:07.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:07.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:07.381][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2022-04-12 10:53:07.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:07.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:07.392][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2022-04-12 10:53:08.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2022-04-12 10:53:08.787][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:08.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2022-04-12 10:53:08.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2022-04-12 10:53:08.862][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2022-04-12 10:53:09.019][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:09.064][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:09.067][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:09.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:09.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:09.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:09.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:09.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:09.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:09.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:09.085][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.088][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.090][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.091][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.108][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:09.111][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:09.112][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.114][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.130][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:09.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:09.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.146][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:09.148][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:09.150][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.152][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.155][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:09.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:09.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.169][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:09.171][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:09.172][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.174][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:09.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.190][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:09.193][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:09.194][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.196][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:09.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:09.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.211][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:09.213][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:09.215][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.217][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.220][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:09.222][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.224][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.226][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.228][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:09.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:09.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:09.245][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.247][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:09.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.264][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:09.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:09.268][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.270][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:09.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:09.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.283][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:09.284][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:09.286][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.289][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.291][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:09.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.306][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:09.308][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:09.309][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.311][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:09.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:09.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:09.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:09.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:09.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:09.418][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2022-04-12 10:53:09.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:09.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:09.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:09.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:09.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:09.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:09.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:09.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:09.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:09.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:09.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:09.460][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2022-04-12 10:53:09.462][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:09.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2022-04-12 10:53:09.469][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:09.471][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:09.473][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:09.476][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:09.478][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:09.480][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:09.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:09.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:09.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:09.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:09.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:09.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:09.507][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[2022-04-12 10:53:09.510][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2022-04-12 10:53:09.516][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:09.518][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:09.521][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2022-04-12 10:53:10.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2022-04-12 10:53:10.616][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:10.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2022-04-12 10:53:10.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2022-04-12 10:53:10.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2022-04-12 10:53:10.701][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:10.741][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:10.743][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:10.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:10.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:10.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:10.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:10.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:10.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:10.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:10.763][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:10.766][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:10.768][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.770][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:10.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:10.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.788][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:10.791][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:10.793][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.794][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.797][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:10.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.813][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:10.815][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:10.817][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.819][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:10.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.837][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:10.839][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:10.841][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.843][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:10.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.870][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:10.871][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:10.873][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.874][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:10.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:10.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.892][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:10.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:10.896][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.897][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.900][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:10.902][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:10.904][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.906][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.909][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:10.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:10.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.925][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:10.927][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:10.929][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.931][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:10.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:10.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.950][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:10.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:10.955][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.957][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:10.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.972][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:10.973][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:10.975][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.976][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.979][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:10.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:10.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:10.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:10.994][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:10.997][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:10.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.000][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:11.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:11.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:11.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:11.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:11.108][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2022-04-12 10:53:11.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:11.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:11.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:11.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:11.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:11.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:11.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:11.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:11.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:11.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:11.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:11.144][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2022-04-12 10:53:11.146][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:11.148][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2022-04-12 10:53:11.150][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:11.151][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:11.153][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:11.155][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:11.157][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:11.159][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:11.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:11.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:11.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:11.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:11.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:11.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:11.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:11.179][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2022-04-12 10:53:11.184][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:11.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:11.188][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2022-04-12 10:53:11.709][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2022-04-12 10:53:12.300][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:12.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2022-04-12 10:53:12.345][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2022-04-12 10:53:12.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2022-04-12 10:53:12.377][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:12.408][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:12.409][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:12.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:12.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:12.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:12.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:12.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:12.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:12.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:12.421][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.423][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.424][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.426][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.440][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:12.441][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:12.442][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.443][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.445][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:12.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:12.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.455][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:12.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:12.457][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.458][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:12.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:12.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:12.476][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.477][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.479][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.494][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:12.496][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:12.497][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.499][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:12.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:12.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:12.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:12.520][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.522][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.524][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:12.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.542][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.544][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:12.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.560][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:12.562][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:12.564][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.565][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:12.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:12.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.581][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:12.583][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:12.585][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.587][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:12.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.599][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:12.601][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:12.602][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.604][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:12.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.619][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:12.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:12.624][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.626][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.628][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:12.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:12.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:12.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:12.727][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2022-04-12 10:53:12.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:12.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:12.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:12.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:12.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:12.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:12.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:12.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:12.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:12.754][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2022-04-12 10:53:12.756][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:12.758][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2022-04-12 10:53:12.760][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:12.762][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:12.764][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:12.766][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:12.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:12.769][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:12.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:12.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:12.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:12.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:12.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:12.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:12.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:12.785][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2022-04-12 10:53:12.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:12.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:12.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2022-04-12 10:53:13.382][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2022-04-12 10:53:13.953][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:13.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2022-04-12 10:53:14.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2022-04-12 10:53:14.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2022-04-12 10:53:14.038][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:14.074][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:14.076][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:14.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:14.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:14.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:14.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:14.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:14.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:14.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:14.088][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.090][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.092][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.107][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:14.109][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:14.112][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.114][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:14.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.131][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:14.133][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:14.135][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.137][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:14.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.155][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:14.157][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:14.159][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.161][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.164][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:14.166][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:14.168][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.170][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.173][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:14.175][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:14.177][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.179][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.181][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:14.184][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.186][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.188][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.190][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.206][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:14.208][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:14.210][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.212][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:14.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:14.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.231][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:14.233][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:14.235][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.238][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:14.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:14.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:14.257][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:14.259][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.261][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.264][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:14.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:14.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.291][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:14.293][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:14.295][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.298][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:14.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:14.389][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2022-04-12 10:53:14.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:14.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:14.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:14.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:14.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:14.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:14.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:14.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:14.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:14.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:14.433][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2022-04-12 10:53:14.435][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:14.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2022-04-12 10:53:14.442][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:14.444][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:14.447][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:14.449][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:14.452][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:14.453][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:14.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:14.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:14.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:14.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:14.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:14.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:14.470][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[2022-04-12 10:53:14.472][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2022-04-12 10:53:14.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:14.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:14.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2022-04-12 10:53:14.977][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2022-04-12 10:53:15.502][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:15.519][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2022-04-12 10:53:15.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2022-04-12 10:53:15.585][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2022-04-12 10:53:15.595][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:15.620][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:15.622][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:15.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:15.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:15.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:15.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:15.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:15.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:15.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:15.634][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.637][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.639][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.653][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:15.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:15.656][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.657][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.658][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:15.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:15.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.672][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:15.673][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:15.675][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.676][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:15.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:15.688][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:15.689][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.690][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.692][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:15.693][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:15.694][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.695][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.697][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:15.698][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:15.700][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.702][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.703][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:15.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.706][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.707][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.709][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.723][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:15.725][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:15.727][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.729][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:15.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:15.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.746][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:15.748][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:15.750][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.752][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:15.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.770][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:15.772][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:15.774][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.776][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.778][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:15.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:15.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.792][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:15.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:15.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.798][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:15.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:15.896][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2022-04-12 10:53:15.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:15.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:15.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:15.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:15.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:15.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:15.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:15.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:15.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:15.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:15.932][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[2022-04-12 10:53:15.935][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2022-04-12 10:53:15.937][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:15.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2022-04-12 10:53:15.940][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:15.942][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:15.943][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:15.944][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:15.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:15.947][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:15.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:15.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:15.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:15.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:15.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:15.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:15.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:15.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2022-04-12 10:53:15.967][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:15.969][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:15.972][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2022-04-12 10:53:16.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2022-04-12 10:53:17.021][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:17.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2022-04-12 10:53:17.071][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2022-04-12 10:53:17.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2022-04-12 10:53:17.109][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:17.146][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:17.148][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:17.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:17.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:17.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:17.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:17.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:17.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:17.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:17.182][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.186][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.188][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.206][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:17.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:17.210][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.212][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:17.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:17.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.230][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:17.232][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:17.234][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.236][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.239][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:17.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:17.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.254][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:17.256][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:17.258][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.260][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:17.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:17.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:17.280][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:17.282][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.284][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.302][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:17.305][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:17.307][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.309][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.311][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:17.314][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.316][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.318][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:17.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:17.339][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:17.341][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.343][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:17.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:17.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.360][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:17.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:17.364][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.366][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:17.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:17.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.385][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:17.387][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:17.389][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.391][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.394][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:17.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.408][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:17.411][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:17.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.415][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.417][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:17.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:17.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:17.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:17.523][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2022-04-12 10:53:17.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:17.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:17.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:17.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:17.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:17.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:17.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:17.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:17.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:17.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:17.561][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2022-04-12 10:53:17.562][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:17.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2022-04-12 10:53:17.566][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:17.567][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:17.568][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:17.570][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:17.571][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:17.572][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:17.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:17.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:17.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:17.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:17.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:17.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:17.583][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2022-04-12 10:53:17.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:17.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:17.592][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2022-04-12 10:53:18.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2022-04-12 10:53:18.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:18.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2022-04-12 10:53:18.791][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2022-04-12 10:53:18.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2022-04-12 10:53:18.829][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:18.865][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:18.867][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:18.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:18.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:18.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:18.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:18.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:18.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:18.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:18.886][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:18.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:18.890][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.891][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:18.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.909][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:18.911][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:18.913][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.915][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:18.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.947][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:18.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:18.950][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.952][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:18.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.971][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:18.974][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:18.976][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.978][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:18.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:18.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:18.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:18.997][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:18.999][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:19.001][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.004][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:19.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:19.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:19.025][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:19.027][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.029][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.031][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:19.034][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.036][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.038][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.040][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:19.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:19.058][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:19.060][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.062][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:19.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:19.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.080][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:19.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:19.085][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.087][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:19.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.106][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:19.108][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:19.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.112][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:19.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.132][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:19.135][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:19.137][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.139][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:19.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:19.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:19.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:19.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:19.234][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2022-04-12 10:53:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:19.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:19.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:19.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:19.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:19.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:19.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:19.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:19.277][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2022-04-12 10:53:19.279][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:19.283][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2022-04-12 10:53:19.285][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:19.287][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:19.290][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:19.291][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:19.293][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:19.295][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:19.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:19.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:19.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:19.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:19.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:19.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:19.320][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[2022-04-12 10:53:19.322][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2022-04-12 10:53:19.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:19.330][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:19.333][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2022-04-12 10:53:19.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2022-04-12 10:53:20.399][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:20.415][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2022-04-12 10:53:20.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2022-04-12 10:53:20.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2022-04-12 10:53:20.476][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:20.509][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:20.511][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:20.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:20.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:20.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:20.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:20.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:20.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:20.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:20.530][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.531][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.532][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.534][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.552][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:20.554][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:20.556][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.558][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:20.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.577][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:20.580][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:20.581][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.583][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:20.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:20.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.602][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:20.604][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:20.622][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.624][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:20.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:20.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.642][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:20.644][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:20.646][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.648][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:20.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:20.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.661][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:20.663][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:20.664][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.665][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.667][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:20.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.669][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.670][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.672][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:20.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.689][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:20.691][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:20.692][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.694][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.709][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:20.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:20.714][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.716][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:20.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:20.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.735][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:20.737][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:20.740][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.742][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.745][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:20.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.763][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:20.765][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:20.768][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.769][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:20.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:20.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:20.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:20.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:20.854][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2022-04-12 10:53:20.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:20.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:20.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:20.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:20.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:20.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:20.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:20.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:20.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:20.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:20.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:20.894][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2022-04-12 10:53:20.895][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:20.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2022-04-12 10:53:20.899][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:20.900][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:20.902][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:20.904][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:20.906][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:20.908][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:20.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:20.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:20.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:20.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:20.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:20.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:20.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:20.924][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2022-04-12 10:53:20.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:20.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:20.930][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2022-04-12 10:53:21.517][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2022-04-12 10:53:22.064][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:22.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2022-04-12 10:53:22.106][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2022-04-12 10:53:22.131][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2022-04-12 10:53:22.138][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:22.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:22.174][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:22.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:22.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:22.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:22.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:22.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:22.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:22.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:22.190][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.193][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.195][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.197][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.209][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:22.211][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:22.213][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.215][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.217][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:22.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.231][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:22.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:22.235][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.237][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:22.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:22.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.254][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:22.256][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:22.258][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.260][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:22.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:22.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:22.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:22.278][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.280][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:22.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:22.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.311][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:22.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:22.314][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.315][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.317][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:22.318][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.319][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.321][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.323][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:22.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.338][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:22.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:22.341][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.343][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:22.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:22.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.361][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:22.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:22.366][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.367][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:22.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:22.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.387][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:22.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:22.391][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.392][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.394][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:22.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:22.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.409][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:22.411][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:22.413][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.415][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:22.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:22.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:22.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:22.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:22.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:22.506][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2022-04-12 10:53:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:22.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:22.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:22.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:22.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:22.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:22.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:22.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:22.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:22.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:22.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:22.530][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2022-04-12 10:53:22.532][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:22.533][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2022-04-12 10:53:22.535][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:22.536][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:22.538][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:22.541][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:22.543][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:22.546][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:22.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:22.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:22.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:22.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:22.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:22.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:22.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:22.561][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2022-04-12 10:53:22.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:22.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:22.570][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2022-04-12 10:53:23.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2022-04-12 10:53:23.650][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:23.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2022-04-12 10:53:23.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2022-04-12 10:53:23.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2022-04-12 10:53:23.729][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:23.765][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:23.768][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:23.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:23.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:23.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:23.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:23.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:23.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:23.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:23.787][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:23.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:23.790][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.791][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:23.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:23.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.810][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:23.811][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:23.812][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.814][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:23.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:23.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.830][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:23.833][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:23.835][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.837][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.839][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:23.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:23.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.854][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:23.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:23.858][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.860][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:23.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:23.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.875][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:23.877][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:23.878][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.879][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:23.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:23.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.894][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:23.895][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:23.896][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.898][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.939][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:23.944][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:23.946][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.948][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.950][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:23.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:23.985][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:23.987][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.989][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:23.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:23.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:23.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:23.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.007][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:24.009][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:24.011][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.013][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:24.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:24.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.032][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:24.034][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:24.036][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.038][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:24.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:24.058][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:24.060][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.062][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.065][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:24.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:24.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:24.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:24.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:24.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.169][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2022-04-12 10:53:24.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.295][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[2022-04-12 10:53:24.300][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:24.303][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:53:24.306][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:24.309][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 10:53:24.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.367][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.TRACE[2022-04-12 10:53:24.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.473][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.TRACE[2022-04-12 10:53:24.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.590][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.TRACE[2022-04-12 10:53:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.634][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.TRACE[2022-04-12 10:53:24.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.713][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[2022-04-12 10:53:24.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.796][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.TRACE[2022-04-12 10:53:24.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.873][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.TRACE[2022-04-12 10:53:24.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:24.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:24.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:24.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:24.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:24.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:24.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:24.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:24.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:24.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:24.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:24.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:25.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:25.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:25.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:25.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:25.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:25.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:25.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:25.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:25.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:25.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:25.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:25.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:25.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:25.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:25.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:25.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:25.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:25.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:25.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:25.294][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[2022-04-12 10:53:25.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:25.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:25.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:25.814][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:26.344][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:26.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1eb5a44d25716d90ff717fcfe93533e3.content"
biodb.TRACE[2022-04-12 10:53:26.389][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1eb5a44d25716d90ff717fcfe93533e3.request"
biodb.DEBUG[2022-04-12 10:53:26.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:26.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:26.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:26.427][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:27.179][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:27.838][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:27.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ef91a3654a792571304ae6f83c5871b.content"
biodb.TRACE[2022-04-12 10:53:27.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ef91a3654a792571304ae6f83c5871b.request"
biodb.DEBUG[2022-04-12 10:53:27.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:27.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:27.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:27.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:27.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:27.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:27.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:27.907][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2022-04-12 10:53:27.909][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:27.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2022-04-12 10:53:27.914][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:27.916][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:27.917][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:27.919][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:27.921][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:27.924][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:27.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:27.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:27.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:27.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:27.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:27.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:27.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:27.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2022-04-12 10:53:27.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:27.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:27.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2022-04-12 10:53:28.551][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2022-04-12 10:53:29.103][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:29.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2022-04-12 10:53:29.152][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2022-04-12 10:53:29.178][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2022-04-12 10:53:29.184][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:29.221][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:29.224][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:29.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:29.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:29.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:29.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:29.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:29.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:29.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:29.245][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.249][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.251][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.267][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:29.270][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:29.272][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.274][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:29.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:29.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.291][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:29.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:29.296][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.298][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.316][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:29.319][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:29.321][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.323][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:29.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.343][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:29.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:29.347][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.349][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:29.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.368][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:29.371][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:29.373][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.375][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.377][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:29.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.392][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:29.394][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:29.396][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.397][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.399][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:29.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.412][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.414][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.416][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.417][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.434][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:29.437][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:29.438][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.440][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:29.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.459][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:29.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:29.471][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.473][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:29.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.489][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:29.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:29.494][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.496][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:29.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:29.599][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2022-04-12 10:53:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:29.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:29.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:29.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:29.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:29.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:29.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:29.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:29.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:29.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:29.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:29.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:29.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:29.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:29.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:29.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:29.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:29.678][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[2022-04-12 10:53:29.681][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2022-04-12 10:53:29.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:29.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2022-04-12 10:53:29.689][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:29.691][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:29.693][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:29.695][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:29.698][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:29.700][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:29.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:29.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:29.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:29.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:29.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:29.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:29.717][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.DEBUG[2022-04-12 10:53:29.719][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2022-04-12 10:53:29.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:29.726][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:29.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2022-04-12 10:53:30.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2022-04-12 10:53:30.961][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:30.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2022-04-12 10:53:31.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2022-04-12 10:53:31.029][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2022-04-12 10:53:31.039][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:31.068][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:31.069][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:31.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.089][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.091][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.093][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.096][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.114][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:31.117][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:31.119][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.121][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:31.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.139][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:31.142][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:31.144][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.146][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:31.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.166][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:31.169][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:31.171][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.173][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:31.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.193][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:31.195][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:31.197][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.198][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.214][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:31.217][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:31.219][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.221][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.224][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:31.227][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:31.229][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.231][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.233][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:31.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:31.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.254][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.256][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.273][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:31.275][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:31.277][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.280][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:31.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:31.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.299][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:31.302][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:31.313][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.316][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.335][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:31.337][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:31.339][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.341][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.343][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:31.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:31.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:31.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:31.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.452][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2022-04-12 10:53:31.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.532][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[2022-04-12 10:53:31.538][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:31.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:53:31.544][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:31.547][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 10:53:31.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.703][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.TRACE[2022-04-12 10:53:31.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.751][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[2022-04-12 10:53:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.958][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[2022-04-12 10:53:31.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:31.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:31.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:31.981][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:31.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:31.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:31.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:31.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:31.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:31.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:31.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:31.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.370][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[2022-04-12 10:53:32.375][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:32.378][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2022-04-12 10:53:32.381][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:32.383][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2022-04-12 10:53:32.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.611][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[2022-04-12 10:53:32.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.646][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[2022-04-12 10:53:32.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.691][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.TRACE[2022-04-12 10:53:32.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.727][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.TRACE[2022-04-12 10:53:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.765][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.TRACE[2022-04-12 10:53:32.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:32.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:32.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:32.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:32.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:32.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:32.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:32.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:32.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:32.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:32.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:32.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:33.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.065][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[2022-04-12 10:53:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:33.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.158][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:33.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:33.177][biodb::testThat]
biodb.INFO [2022-04-12 10:53:33.179][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-04-12 10:53:33.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:33.181][biodb::testThat]
biodb.TRACE[2022-04-12 10:53:33.186][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:33.489][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[2022-04-12 10:53:33.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:33.498][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1e3885f0c8b7bc081513880959401862".
biodb.TRACE[2022-04-12 10:53:33.500][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:33.503][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content".
biodb.DEBUG[2022-04-12 10:53:33.508][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[2022-04-12 10:53:33.514][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:33.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4b7e19492b2d1086a5dba1710a3b39b".
biodb.TRACE[2022-04-12 10:53:33.520][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:33.523][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content".
biodb.DEBUG[2022-04-12 10:53:33.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:33.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:33.574][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:33.577][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d57f841033be8ab371045edb0388ed60".
biodb.TRACE[2022-04-12 10:53:33.579][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:33.582][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content".
biodb.DEBUG[2022-04-12 10:53:33.587][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:33.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:33.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.617][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:33.619][private$selectFields]
biodb.TRACE[2022-04-12 10:53:33.621][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:33.622][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:33.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:33.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.629][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.631][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.633][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.635][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.637][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.639][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.641][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:33.643][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:33.645][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.648][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.650][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.652][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.654][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:33.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:33.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.698][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:33.700][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:33.702][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:33.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:33.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:33.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:33.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:33.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:33.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:33.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:33.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:33.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:33.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:34.103][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[2022-04-12 10:53:34.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:34.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:34.116][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:34.935][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:35.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:35.652][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content"
biodb.TRACE[2022-04-12 10:53:35.698][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.request"
biodb.DEBUG[2022-04-12 10:53:35.721][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:35.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:35.730][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:35.733][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:36.287][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:36.955][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:36.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content"
biodb.TRACE[2022-04-12 10:53:37.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.request"
biodb.DEBUG[2022-04-12 10:53:37.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:37.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:37.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.122][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[2022-04-12 10:53:37.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:37.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:37.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:37.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:37.249][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:37.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:37.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.315][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.316][private$selectFields]
biodb.TRACE[2022-04-12 10:53:37.318][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:37.320][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:37.322][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.326][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.328][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.329][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.331][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.334][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.336][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.338][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.339][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.341][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.342][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.344][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.345][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.347][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:37.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.366][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 10:53:37.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:37.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.479][private$selectFields]
biodb.TRACE[2022-04-12 10:53:37.481][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:37.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:37.485][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.498][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.500][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.502][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.503][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.504][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.505][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.507][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.528][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.532][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.534][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.536][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:37.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.563][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:37.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:37.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.593][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.594][private$selectFields]
biodb.TRACE[2022-04-12 10:53:37.596][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:37.598][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:37.599][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.601][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.605][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.607][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.614][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.616][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.620][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:37.623][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.627][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.629][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.631][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:37.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:37.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.655][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 10:53:37.656][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:37.658][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:37.673][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:37.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:37.684][biodb::testThat]
biodb.INFO [2022-04-12 10:53:37.686][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-04-12 10:53:37.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:37.690][biodb::testThat]
biodb.TRACE[2022-04-12 10:53:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:37.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:37.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:37.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:37.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:37.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:37.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:37.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:37.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:37.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:37.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:37.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:38.148][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[2022-04-12 10:53:38.153][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:38.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1e3885f0c8b7bc081513880959401862".
biodb.TRACE[2022-04-12 10:53:38.157][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:38.159][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content".
biodb.DEBUG[2022-04-12 10:53:38.164][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[2022-04-12 10:53:38.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:38.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4b7e19492b2d1086a5dba1710a3b39b".
biodb.TRACE[2022-04-12 10:53:38.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:38.175][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content".
biodb.DEBUG[2022-04-12 10:53:38.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:38.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:38.216][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:38.221][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:38.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d57f841033be8ab371045edb0388ed60".
biodb.TRACE[2022-04-12 10:53:38.227][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:38.229][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content".
biodb.DEBUG[2022-04-12 10:53:38.233][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:38.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.257][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.258][private$selectFields]
biodb.TRACE[2022-04-12 10:53:38.259][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:38.261][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:38.262][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.264][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.266][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.268][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.269][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.275][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.277][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.279][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.281][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.283][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.287][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.289][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.291][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:38.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:38.322][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:38.332][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:38.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:38.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:38.630][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[2022-04-12 10:53:38.635][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:38.638][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c60f2116f91d4ce61370ae6298305b49".
biodb.TRACE[2022-04-12 10:53:38.641][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:38.643][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content".
biodb.DEBUG[2022-04-12 10:53:38.649][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[2022-04-12 10:53:38.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:38.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "921bb2fccd1f3497458cb7cf8fd2ffda".
biodb.TRACE[2022-04-12 10:53:38.660][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:38.663][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content".
biodb.DEBUG[2022-04-12 10:53:38.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:38.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:38.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:38.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:38.782][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:38.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.816][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.817][private$selectFields]
biodb.TRACE[2022-04-12 10:53:38.819][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:38.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:38.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.829][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.830][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.832][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.838][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.839][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.841][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.842][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.844][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.846][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.847][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.849][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:38.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.874][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 10:53:38.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.903][private$selectFields]
biodb.TRACE[2022-04-12 10:53:38.904][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:38.905][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:38.907][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.908][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.909][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.910][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.912][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.916][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.917][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.919][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.921][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.923][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.928][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.929][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.931][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:38.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.956][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:38.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:38.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:38.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:38.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:38.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:38.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:38.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:38.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:38.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:38.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.987][private$selectFields]
biodb.TRACE[2022-04-12 10:53:38.989][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:38.991][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:38.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:38.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.997][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:38.998][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.000][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.002][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.004][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.006][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.008][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.010][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.012][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.024][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.027][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.029][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 10:53:39.053][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:39.055][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:39.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:39.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:39.078][biodb::testThat]
biodb.INFO [2022-04-12 10:53:39.080][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-04-12 10:53:39.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:39.083][biodb::testThat]
biodb.TRACE[2022-04-12 10:53:39.090][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-04-12 10:53:39.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-04-12 10:53:39.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.135][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[2022-04-12 10:53:39.328][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[2022-04-12 10:53:39.333][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:39.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1e3885f0c8b7bc081513880959401862".
biodb.TRACE[2022-04-12 10:53:39.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:39.340][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1e3885f0c8b7bc081513880959401862.content".
biodb.DEBUG[2022-04-12 10:53:39.345][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[2022-04-12 10:53:39.350][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:39.352][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4b7e19492b2d1086a5dba1710a3b39b".
biodb.TRACE[2022-04-12 10:53:39.354][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:39.357][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f4b7e19492b2d1086a5dba1710a3b39b.content".
biodb.DEBUG[2022-04-12 10:53:39.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.399][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:39.405][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:39.408][cch$loadFileContent] Trying to load 1 files from cache: [1]: "d57f841033be8ab371045edb0388ed60".
biodb.TRACE[2022-04-12 10:53:39.410][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:39.412][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d57f841033be8ab371045edb0388ed60.content".
biodb.DEBUG[2022-04-12 10:53:39.416][private$bdb$entriesToDataframe] 1 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:39.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.432][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.TRACE[2022-04-12 10:53:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.446][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.448][private$selectFields]
biodb.TRACE[2022-04-12 10:53:39.450][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:39.451][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:39.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.457][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.458][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.459][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.463][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.464][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.466][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.468][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.473][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.475][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.477][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:39.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:39.503][private$entriesToListOfDataframes] Converted 1 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:39.505][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:39.809][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[2022-04-12 10:53:39.814][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:39.817][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c60f2116f91d4ce61370ae6298305b49".
biodb.TRACE[2022-04-12 10:53:39.818][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:39.821][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c60f2116f91d4ce61370ae6298305b49.content".
biodb.DEBUG[2022-04-12 10:53:39.826][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[2022-04-12 10:53:39.831][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:39.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "921bb2fccd1f3497458cb7cf8fd2ffda".
biodb.TRACE[2022-04-12 10:53:39.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:39.840][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/921bb2fccd1f3497458cb7cf8fd2ffda.content".
biodb.DEBUG[2022-04-12 10:53:39.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:39.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:39.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:39.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:39.952][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-04-12 10:53:39.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:39.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:39.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:39.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:39.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:39.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:39.966][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[2022-04-12 10:53:39.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:39.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:39.988][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.990][private$selectFields]
biodb.TRACE[2022-04-12 10:53:39.992][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:39.994][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:39.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:39.998][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.000][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.002][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.003][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.005][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.009][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.011][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.015][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.016][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.020][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.021][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.023][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:40.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.047][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2022-04-12 10:53:40.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:40.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:40.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:40.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:40.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:40.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:40.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:40.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.077][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.079][private$selectFields]
biodb.TRACE[2022-04-12 10:53:40.080][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:40.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:40.083][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.085][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.089][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.091][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.096][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.097][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.100][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.103][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.105][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.107][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.109][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.132][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2022-04-12 10:53:40.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:40.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:40.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:40.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:40.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:40.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:40.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.165][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.167][private$selectFields]
biodb.TRACE[2022-04-12 10:53:40.169][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-04-12 10:53:40.171][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-04-12 10:53:40.172][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.174][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.177][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.179][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.181][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.183][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.187][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.189][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.191][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.193][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2022-04-12 10:53:40.195][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.198][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.200][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.202][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2022-04-12 10:53:40.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:40.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:40.227][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2022-04-12 10:53:40.229][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-04-12 10:53:40.231][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-04-12 10:53:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:40.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-04-12 10:53:40.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:40.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-04-12 10:53:40.276][biodb::testThat]
biodb.INFO [2022-04-12 10:53:40.278][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2022-04-12 10:53:40.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:40.282][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:40.286][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-04-12 10:53:40.288][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:40.291][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-04-12 10:53:40.294][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:40.296][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:40.298][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:40.300][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:40.302][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:40.304][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:40.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:40.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:40.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:40.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:40.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:40.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:40.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:40.331][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2022-04-12 10:53:40.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:40.339][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:40.341][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2022-04-12 10:53:40.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2022-04-12 10:53:41.522][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:41.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2022-04-12 10:53:41.624][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2022-04-12 10:53:41.673][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2022-04-12 10:53:41.692][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:41.731][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:41.733][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:41.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:41.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:41.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:41.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:41.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:41.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:41.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:41.750][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.754][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.756][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.783][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:41.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:41.787][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.789][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.791][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:41.793][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:41.795][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.796][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.799][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:41.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:41.802][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.804][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.805][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:41.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:41.809][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.810][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.812][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:41.814][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:41.816][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.817][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.818][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:41.820][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:41.822][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.824][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.827][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:41.829][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:41.831][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.832][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.833][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:41.834][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:41.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.838][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.841][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:41.843][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:41.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.846][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.848][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:41.850][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:41.851][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.853][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:41.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:41.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:41.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:41.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:41.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:41.942][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2022-04-12 10:53:41.943][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.INFO [2022-04-12 10:53:41.954][biodb::testThat]
biodb.INFO [2022-04-12 10:53:41.955][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-04-12 10:53:41.957][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:41.958][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:41.973][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2022-04-12 10:53:41.975][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2022-04-12 10:53:41.977][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2022-04-12 10:53:41.980][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2022-04-12 10:53:41.982][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2022-04-12 10:53:41.985][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2022-04-12 10:53:41.987][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:41.989][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:41.991][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:41.993][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:41.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:42.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:42.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:42.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:42.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:42.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:42.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:42.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2022-04-12 10:53:42.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:42.020][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:42.023][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2022-04-12 10:53:42.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2022-04-12 10:53:43.199][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:43.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2022-04-12 10:53:43.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2022-04-12 10:53:43.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:43.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:43.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:43.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:43.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:43.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:43.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:43.325][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2022-04-12 10:53:43.330][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:43.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:43.335][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2022-04-12 10:53:43.919][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2022-04-12 10:53:44.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:44.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2022-04-12 10:53:44.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2022-04-12 10:53:44.698][private$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[2022-04-12 10:53:44.722][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:44.766][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2022-04-12 10:53:44.769][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:44.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:44.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:44.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:44.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:44.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:44.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:44.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:44.788][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.791][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.793][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.795][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.824][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:44.826][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:44.828][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.830][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.832][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:44.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:44.836][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.838][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:44.843][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:44.845][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.846][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.849][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:44.851][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:44.853][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.855][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.857][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:44.859][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:44.861][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.863][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.865][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:44.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:44.869][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.871][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.873][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:44.875][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:44.877][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.879][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.882][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:44.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:44.886][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.888][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.891][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:44.893][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:44.895][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.896][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:44.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:44.902][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.904][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:44.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:44.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:44.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:44.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:44.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:44.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:44.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:44.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:44.996][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:44.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.001][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.003][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.031][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:45.033][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:45.035][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.037][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:45.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.072][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:45.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:45.077][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.078][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.080][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:45.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:45.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:45.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:45.110][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.111][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:45.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:45.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.137][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.140][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.141][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.143][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.169][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.171][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.172][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.174][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.176][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.200][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:45.202][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:45.204][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.205][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.207][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:45.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.231][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.233][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.235][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.236][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.260][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:45.261][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:45.263][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.264][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:45.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:45.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.292][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:45.294][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:45.296][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.298][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.322][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:45.324][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:45.325][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.326][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:45.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:45.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:45.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:45.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:45.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:45.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:45.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:45.433][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.436][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.437][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.461][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:45.539][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:45.551][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.553][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:45.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.728][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:45.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:45.731][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.732][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:45.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.748][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:45.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:45.751][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.752][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.772][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.773][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:45.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.794][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.795][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.796][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.797][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.799][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:45.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.818][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:45.820][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:45.821][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.822][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:45.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.850][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.854][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.857][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:45.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.881][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:45.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:45.885][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.886][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:45.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:45.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:45.918][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:45.919][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.921][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.946][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:45.948][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:45.950][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.952][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:45.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:45.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:45.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:45.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:45.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:46.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:46.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:46.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:46.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:46.103][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2022-04-12 10:53:46.104][self$createEntryFromContent] Found %d entry/ies without an accession number. Set it/them to NULL.1
biodb.DEBUG[2022-04-12 10:53:46.106][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-04-12 10:53:46.123][biodb::testThat]
biodb.INFO [2022-04-12 10:53:46.124][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2022-04-12 10:53:46.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:46.127][biodb::testThat]
biodb.INFO [2022-04-12 10:53:46.169][biodb::testThat]
biodb.INFO [2022-04-12 10:53:46.171][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2022-04-12 10:53:46.173][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:46.175][biodb::testThat]
biodb.INFO [2022-04-12 10:53:46.185][biodb::testThat]
biodb.INFO [2022-04-12 10:53:46.187][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2022-04-12 10:53:46.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:46.190][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:46.194][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:46.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:46.209][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:46.211][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:46.825][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:47.732][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:47.769][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/abfdad4f2c265f1c152262cabd0cf864.content"
biodb.TRACE[2022-04-12 10:53:47.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/abfdad4f2c265f1c152262cabd0cf864.request"
biodb.INFO [2022-04-12 10:53:47.863][biodb::testThat]
biodb.INFO [2022-04-12 10:53:47.865][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2022-04-12 10:53:47.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:47.869][biodb::testThat]
biodb.ERROR[2022-04-12 10:53:47.891][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-04-12 10:53:47.918][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-04-12 10:53:47.932][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:47.934][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 10:53:47.935][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 10:53:47.936][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:47.937][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:47.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:47.941][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:47.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:47.944][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:47.946][FUN] Functions in observer BiodbConfig: [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 [2022-04-12 10:53:47.963][biodb::testContext]
biodb.INFO [2022-04-12 10:53:47.965][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:47.967][biodb::testContext] Test context - Test conversions
biodb.INFO [2022-04-12 10:53:47.968][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:47.970][biodb::testContext]
biodb.INFO [2022-04-12 10:53:47.990][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:47.992][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:48.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:48.002][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:53:48.004][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.011][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:53:48.012][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.018][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:53:48.020][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.025][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:53:48.027][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:53:48.029][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:53:48.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.036][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:53:48.038][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:53:48.040][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.047][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:53:48.049][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:53:48.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.054][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:53:48.056][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:53:48.057][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:53:48.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.064][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:53:48.066][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.071][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[2022-04-12 10:53:48.072][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:53:48.074][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:53:48.076][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:53:48.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.081][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:48.083][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:53:48.092][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:53:48.094][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:53:48.096][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:53:48.098][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:53:48.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.106][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:53:48.108][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:53:48.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.115][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:53:48.117][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:53:48.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.123][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:53:48.125][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:53:48.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.132][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:53:48.134][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:53:48.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.140][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:53:48.142][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:53:48.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.148][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:48.150][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:53:48.161][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:53:48.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.166][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:53:48.168][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:53:48.170][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:53:48.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.175][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:53:48.178][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.179][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:53:48.181][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.182][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:48.184][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.185][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.187][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.191][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:48.193][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:48.195][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.197][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:53:48.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:48.200][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.201][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.202][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:48.202][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:48.202][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:48.202][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:48.202][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:48.203][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:48.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:48.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.213][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.215][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:48.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:48.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.222][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.224][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:53:48.227][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.229][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:48.230][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.232][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:48.233][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.234][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.235][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.236][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.238][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:48.239][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:48.241][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.243][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:53:48.244][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:48.245][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.249][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:48.249][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:48.249][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:48.249][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:48.249][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:48.251][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:48.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.257][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:48.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.264][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.266][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:48.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:48.269][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.271][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.273][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:53:48.277][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.279][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:53:48.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:48.285][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.289][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.293][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:48.295][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:48.297][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.299][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:53:48.301][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:48.302][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.304][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.306][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:48.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:48.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.318][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.320][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.321][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:48.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:48.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.326][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.328][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:53:48.331][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.333][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:48.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.337][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:48.339][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.341][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.343][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.347][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:48.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:48.349][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.351][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:53:48.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:48.355][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.357][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:48.359][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.361][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:48.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:48.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:48.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:48.495][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:48.508][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:48.512][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:48.514][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:48.516][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:48.519][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:48.521][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.523][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[2022-04-12 10:53:48.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.563][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[2022-04-12 10:53:48.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.665][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[2022-04-12 10:53:48.667][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:48.668][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:48.671][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:48.673][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:48.676][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:48.677][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:48.679][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:48.681][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:48.683][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:48.686][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:48.688][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:48.690][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:48.692][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:48.695][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:48.698][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:48.701][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:48.703][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:48.706][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:48.708][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:48.711][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:48.713][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:48.716][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:48.718][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:48.721][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:48.723][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:48.726][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:48.728][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:48.731][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:48.734][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:48.736][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:48.739][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:48.742][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:48.745][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:48.748][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:48.750][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:48.753][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:48.756][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:48.760][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:48.762][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:48.765][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:48.768][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:48.771][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:48.773][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:48.776][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:48.779][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:48.782][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:48.784][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:48.787][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:48.790][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:48.793][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:48.796][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:48.799][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:48.802][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:48.806][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:48.809][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:48.812][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:48.814][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:48.817][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:48.819][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:48.822][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:48.824][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:48.826][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:48.828][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:48.832][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:48.835][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:48.838][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:48.841][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:48.845][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:48.848][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:48.859][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:48.861][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:48.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:48.867][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:48.870][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:48.873][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:48.875][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:48.878][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:48.881][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:48.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:48.887][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:48.889][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:48.892][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:48.895][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:48.898][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:48.901][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:48.903][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:48.904][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.927][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[2022-04-12 10:53:48.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.949][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[2022-04-12 10:53:48.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.958][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.DEBUG[2022-04-12 10:53:48.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.966][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[2022-04-12 10:53:48.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:48.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:48.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:48.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:48.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:48.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:48.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:48.999][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[2022-04-12 10:53:49.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.036][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[2022-04-12 10:53:49.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.056][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[2022-04-12 10:53:49.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:49.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.087][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:49.090][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 10:53:49.093][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:49.095][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:49.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:49.099][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:49.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:49.103][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:49.105][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:49.107][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 10:53:49.109][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:53:49.110][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:49.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:49.112][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 10:53:49.114][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 10:53:49.115][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 10:53:49.116][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:49.117][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:49.117][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:49.117][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:49.119][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:53:49.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:49.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:49.122][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:49.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:49.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:49.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:49.126][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:49.126][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 10:53:49.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:49.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:49.130][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:49.131][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 10:53:49.131][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 10:53:49.155][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:49.157][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:49.159][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 10:53:49.161][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:49.163][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:49.165][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:49.169][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 10:53:49.170][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 10:53:49.172][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 10:53:49.174][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 10:53:49.175][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:49.177][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:49.179][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 10:53:49.181][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 10:53:49.183][biodb::testThat]
biodb.INFO [2022-04-12 10:53:49.185][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2022-04-12 10:53:49.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:49.189][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:49.195][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 10:53:49.202][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.204][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 10:53:49.206][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.209][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 10:53:49.214][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[2022-04-12 10:53:49.219][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.222][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-04-12 10:53:49.225][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.228][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-04-12 10:53:49.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.244][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[2022-04-12 10:53:49.249][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-04-12 10:53:49.255][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.258][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-04-12 10:53:49.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.273][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.DEBUG[2022-04-12 10:53:49.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.317][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[2022-04-12 10:53:49.323][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.326][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-04-12 10:53:49.328][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.330][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-04-12 10:53:49.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.347][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[2022-04-12 10:53:49.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-04-12 10:53:49.355][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.358][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-04-12 10:53:49.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.383][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[2022-04-12 10:53:49.387][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2022-04-12 10:53:49.391][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.393][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2022-04-12 10:53:49.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.411][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[2022-04-12 10:53:49.417][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2022-04-12 10:53:49.422][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2022-04-12 10:53:49.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:49.444][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[2022-04-12 10:53:49.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:49.452][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2022-04-12 10:53:49.454][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:49.457][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2022-04-12 10:53:49.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:49.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:49.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:49.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:49.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:49.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:49.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 10:53:49.484][biodb::testThat]
biodb.INFO [2022-04-12 10:53:49.485][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2022-04-12 10:53:49.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:49.487][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:49.491][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[2022-04-12 10:53:49.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:49.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:49.498][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:50.122][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:50.742][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:50.792][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3d0a94707e73df0ba810a5a87df958c6.content"
biodb.TRACE[2022-04-12 10:53:50.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3d0a94707e73df0ba810a5a87df958c6.request"
biodb.DEBUG[2022-04-12 10:53:50.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:50.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:50.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:50.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:50.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:50.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:50.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:50.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:50.880][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:50.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:50.885][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:51.440][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:52.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:52.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c23a09621704f6dcea62f90283def982.content"
biodb.TRACE[2022-04-12 10:53:52.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c23a09621704f6dcea62f90283def982.request"
biodb.DEBUG[2022-04-12 10:53:52.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:52.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 10:53:52.198][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:52.201][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 10:53:52.203][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 10:53:52.204][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:52.206][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.209][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.212][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.213][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.INFO [2022-04-12 10:53:52.217][biodb::testContext]
biodb.INFO [2022-04-12 10:53:52.219][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:52.220][biodb::testContext] Test context - Test web services
biodb.INFO [2022-04-12 10:53:52.221][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:52.222][biodb::testContext]
biodb.INFO [2022-04-12 10:53:52.241][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:52.244][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:52.252][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:52.253][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:53:52.255][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.261][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:53:52.263][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.268][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[2022-04-12 10:53:52.270][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:53:52.272][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.278][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:53:52.280][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:53:52.282][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:53:52.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.287][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:53:52.289][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:53:52.290][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.294][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:53:52.296][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:53:52.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.302][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:53:52.303][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:53:52.312][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:53:52.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.318][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:53:52.319][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.325][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:53:52.326][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:53:52.327][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:53:52.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.333][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:52.335][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:53:52.336][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:53:52.338][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:53:52.339][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:53:52.341][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:53:52.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.346][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:53:52.348][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:53:52.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.355][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:53:52.357][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:53:52.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.363][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:53:52.364][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:53:52.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.369][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:53:52.370][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:53:52.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.377][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:53:52.379][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:53:52.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.385][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:52.387][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:53:52.397][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:53:52.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.402][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:53:52.403][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:53:52.404][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:53:52.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.410][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:53:52.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.414][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-04-12 10:53:52.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:52.418][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.419][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.420][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.422][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.423][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:52.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:52.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.429][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:53:52.430][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:52.432][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.435][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:52.435][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:52.435][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:52.435][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:52.435][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:52.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:52.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:52.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.446][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:52.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:52.449][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.451][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.453][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:53:52.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.459][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:52.461][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:52.464][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.470][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.472][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:52.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:52.475][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.476][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:53:52.478][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:52.479][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:52.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:52.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:52.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:52.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:52.485][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:52.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:52.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.494][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.495][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.497][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:52.498][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:52.499][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.500][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.502][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:53:52.505][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.507][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-04-12 10:53:52.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:52.512][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.516][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.518][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.520][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:52.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:52.524][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.526][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:53:52.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:52.530][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.532][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.533][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.535][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:52.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:52.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.544][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:52.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:52.549][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.551][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.553][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:53:52.557][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.559][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:52.561][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:52.565][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.566][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.570][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.572][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:52.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:52.575][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.576][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:53:52.578][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:52.579][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.581][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:52.582][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:52.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:52.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:52.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:52.599][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:52.601][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:52.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:52.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:52.608][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:52.611][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:52.612][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.678][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[2022-04-12 10:53:52.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.687][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[2022-04-12 10:53:52.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.717][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.DEBUG[2022-04-12 10:53:52.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.722][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[2022-04-12 10:53:52.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.727][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[2022-04-12 10:53:52.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.739][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:52.742][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:52.745][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:52.748][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:52.750][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:52.753][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:52.755][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:52.758][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:52.760][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:52.762][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:52.764][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:52.767][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:52.769][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:52.771][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:52.772][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:52.774][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:52.776][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:52.778][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:52.780][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:52.783][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:52.786][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:52.788][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:52.791][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:52.794][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:52.797][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:52.800][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:52.803][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:52.804][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:52.807][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:52.810][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:52.812][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:52.814][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:52.816][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:52.819][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:52.822][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:52.825][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:52.827][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:52.829][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:52.831][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:52.834][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:52.837][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:52.839][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:52.841][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:52.844][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:52.846][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:52.848][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:52.851][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:52.853][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:52.856][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:52.859][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:52.862][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:52.865][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:52.866][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:52.868][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:52.870][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:52.872][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:52.875][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:52.877][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:52.887][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:52.890][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:52.894][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:52.896][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:52.898][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:52.900][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:52.902][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:52.905][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:52.908][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:52.911][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:52.914][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:52.916][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:52.919][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:52.922][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:52.925][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:52.927][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:52.929][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:52.932][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:52.935][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:52.938][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:52.940][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:52.943][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:52.945][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:52.948][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:52.950][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:52.953][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:52.956][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:52.958][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:52.960][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.962][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:52.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:52.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:52.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:52.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:52.994][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[2022-04-12 10:53:52.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:52.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:52.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.036][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[2022-04-12 10:53:53.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.047][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[2022-04-12 10:53:53.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.071][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[2022-04-12 10:53:53.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.094][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[2022-04-12 10:53:53.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:53.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:53.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:53.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:53.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:53.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:53.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:53.129][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:53.132][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 10:53:53.136][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:53.137][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:53.139][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:53.140][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:53.143][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:53.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:53.146][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:53.148][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 10:53:53.150][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:53:53.152][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:53.154][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:53.155][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 10:53:53.157][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 10:53:53.160][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 10:53:53.163][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:53.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:53.171][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:53.171][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:53.173][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:53:53.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:53.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:53.180][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:53.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:53.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:53.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:53.187][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:53.187][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 10:53:53.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:53.191][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:53.193][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:53.195][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 10:53:53.195][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 10:53:53.198][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:53.201][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:53.204][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 10:53:53.207][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:53.210][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:53.213][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:53.220][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 10:53:53.222][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 10:53:53.224][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 10:53:53.226][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 10:53:53.228][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:53.230][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:53.232][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 10:53:53.234][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 10:53:53.236][biodb::testThat]
biodb.INFO [2022-04-12 10:53:53.238][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2022-04-12 10:53:53.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:53.242][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:53.248][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 10:53:53.253][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:53.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 10:53:53.256][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:53.258][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 10:53:53.262][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[2022-04-12 10:53:53.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:53.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:53.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2022-04-12 10:53:53.805][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2022-04-12 10:53:54.442][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:54.477][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2022-04-12 10:53:54.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2022-04-12 10:53:54.531][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:54.532][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 10:53:54.534][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 10:53:54.535][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:54.536][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:54.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:54.538][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.541][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-04-12 10:53:54.547][biodb::testContext]
biodb.INFO [2022-04-12 10:53:54.548][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:54.549][biodb::testContext] Test context - Non regression tests
biodb.INFO [2022-04-12 10:53:54.550][biodb::testContext] ********************************************************************************
biodb.INFO [2022-04-12 10:53:54.552][biodb::testContext]
biodb.INFO [2022-04-12 10:53:54.566][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:54.568][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:54.573][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:54.574][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-04-12 10:53:54.575][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.579][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-04-12 10:53:54.581][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.585][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-04-12 10:53:54.586][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.591][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-04-12 10:53:54.592][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-04-12 10:53:54.593][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-04-12 10:53:54.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.598][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-04-12 10:53:54.599][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-04-12 10:53:54.601][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.607][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[2022-04-12 10:53:54.609][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-04-12 10:53:54.610][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-04-12 10:53:54.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.615][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-04-12 10:53:54.616][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-04-12 10:53:54.617][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-04-12 10:53:54.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.621][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[2022-04-12 10:53:54.623][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-04-12 10:53:54.625][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.632][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-04-12 10:53:54.634][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-04-12 10:53:54.636][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-04-12 10:53:54.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.650][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[2022-04-12 10:53:54.652][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:54.654][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-04-12 10:53:54.656][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-04-12 10:53:54.658][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-04-12 10:53:54.661][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-04-12 10:53:54.663][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-04-12 10:53:54.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.669][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-04-12 10:53:54.671][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-04-12 10:53:54.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.676][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-04-12 10:53:54.678][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-04-12 10:53:54.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.684][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-04-12 10:53:54.686][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-04-12 10:53:54.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.691][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[2022-04-12 10:53:54.693][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-04-12 10:53:54.695][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-04-12 10:53:54.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.701][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-04-12 10:53:54.703][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-04-12 10:53:54.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.707][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-04-12 10:53:54.709][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-04-12 10:53:54.717][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2022-04-12 10:53:54.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.724][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-04-12 10:53:54.726][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-04-12 10:53:54.728][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-04-12 10:53:54.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.733][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-04-12 10:53:54.736][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.739][self$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[2022-04-12 10:53:54.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.743][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:54.744][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.745][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.749][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:54.750][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:54.752][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.754][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-04-12 10:53:54.756][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:54.757][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.758][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:54.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:54.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:54.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:54.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:54.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:54.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:54.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.774][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:54.777][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:54.779][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.781][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.784][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-04-12 10:53:54.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.789][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:54.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:54.792][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.795][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.797][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:54.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:54.801][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.803][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-04-12 10:53:54.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:54.807][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.809][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.810][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:54.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:54.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:54.810][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-04-12 10:53:54.810][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-04-12 10:53:54.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:54.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:54.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.822][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.823][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.824][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:54.825][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:54.826][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.828][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.829][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-04-12 10:53:54.831][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.833][self$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[2022-04-12 10:53:54.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.837][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:54.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.841][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.846][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-04-12 10:53:54.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:54.850][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.852][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-04-12 10:53:54.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:54.855][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.858][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.860][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:54.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:54.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.869][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.871][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:54.875][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:54.877][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.878][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.879][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-04-12 10:53:54.881][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.884][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-04-12 10:53:54.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.887][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:54.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.897][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-04-12 10:53:54.898][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:54.900][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.902][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-04-12 10:53:54.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:54.905][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:54.907][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.909][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-04-12 10:53:54.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.913][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:54.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:54.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:54.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:54.919][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:54.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:54.924][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:54.925][self$setPropertyValue]
biodb.DEBUG[2022-04-12 10:53:54.928][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:54.929][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.930][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[2022-04-12 10:53:54.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.942][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[2022-04-12 10:53:54.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.949][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[2022-04-12 10:53:54.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.957][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.DEBUG[2022-04-12 10:53:54.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.965][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[2022-04-12 10:53:54.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.983][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[2022-04-12 10:53:54.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:54.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:54.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:54.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:54.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:54.999][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[2022-04-12 10:53:55.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.045][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[2022-04-12 10:53:55.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.062][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-04-12 10:53:55.064][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-04-12 10:53:55.067][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-04-12 10:53:55.069][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-04-12 10:53:55.072][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:55.075][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-04-12 10:53:55.078][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:55.080][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:55.082][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-04-12 10:53:55.085][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-04-12 10:53:55.088][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:55.091][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-04-12 10:53:55.094][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-04-12 10:53:55.096][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-04-12 10:53:55.098][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-04-12 10:53:55.100][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-04-12 10:53:55.103][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-04-12 10:53:55.106][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-04-12 10:53:55.109][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:55.113][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-04-12 10:53:55.116][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-04-12 10:53:55.119][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-04-12 10:53:55.122][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-04-12 10:53:55.125][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-04-12 10:53:55.129][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-04-12 10:53:55.132][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-04-12 10:53:55.135][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-04-12 10:53:55.138][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-04-12 10:53:55.140][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-04-12 10:53:55.142][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-04-12 10:53:55.144][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-04-12 10:53:55.146][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-04-12 10:53:55.148][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-04-12 10:53:55.150][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-04-12 10:53:55.151][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-04-12 10:53:55.154][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-04-12 10:53:55.155][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-04-12 10:53:55.157][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-04-12 10:53:55.160][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-04-12 10:53:55.162][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-04-12 10:53:55.164][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-04-12 10:53:55.167][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-04-12 10:53:55.169][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-04-12 10:53:55.172][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-04-12 10:53:55.175][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-04-12 10:53:55.177][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-04-12 10:53:55.180][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-04-12 10:53:55.182][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-04-12 10:53:55.185][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-04-12 10:53:55.188][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-04-12 10:53:55.190][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-04-12 10:53:55.193][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-04-12 10:53:55.196][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-04-12 10:53:55.199][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-04-12 10:53:55.201][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-04-12 10:53:55.203][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-04-12 10:53:55.205][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-04-12 10:53:55.208][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-04-12 10:53:55.211][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-04-12 10:53:55.213][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-04-12 10:53:55.216][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-04-12 10:53:55.219][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-04-12 10:53:55.229][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-04-12 10:53:55.232][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-04-12 10:53:55.234][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-04-12 10:53:55.236][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-04-12 10:53:55.238][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:55.240][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:55.243][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-04-12 10:53:55.245][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-04-12 10:53:55.248][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-04-12 10:53:55.251][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-04-12 10:53:55.254][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-04-12 10:53:55.257][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-04-12 10:53:55.259][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-04-12 10:53:55.262][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-04-12 10:53:55.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-04-12 10:53:55.267][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-04-12 10:53:55.269][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-04-12 10:53:55.271][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-04-12 10:53:55.273][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-04-12 10:53:55.275][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-04-12 10:53:55.277][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-04-12 10:53:55.279][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-04-12 10:53:55.281][initialize] This is biodb version 1.2.2.
biodb.DEBUG[2022-04-12 10:53:55.282][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-04-12 10:53:55.283][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.286][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.351][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[2022-04-12 10:53:55.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.370][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[2022-04-12 10:53:55.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.381][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[2022-04-12 10:53:55.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.391][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[2022-04-12 10:53:55.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.432][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[2022-04-12 10:53:55.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-04-12 10:53:55.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.450][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[2022-04-12 10:53:55.452][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2022-04-12 10:53:55.454][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2022-04-12 10:53:55.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:55.458][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-04-12 10:53:55.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:55.462][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-04-12 10:53:55.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:55.464][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-04-12 10:53:55.465][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:55.467][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2022-04-12 10:53:55.469][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2022-04-12 10:53:55.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-04-12 10:53:55.473][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:55.476][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2022-04-12 10:53:55.478][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2022-04-12 10:53:55.480][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2022-04-12 10:53:55.482][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-04-12 10:53:55.484][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-04-12 10:53:55.484][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-04-12 10:53:55.484][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-04-12 10:53:55.486][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-04-12 10:53:55.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:55.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:55.498][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-04-12 10:53:55.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-04-12 10:53:55.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-04-12 10:53:55.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-04-12 10:53:55.507][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:55.507][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2022-04-12 10:53:55.509][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-04-12 10:53:55.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-04-12 10:53:55.511][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-04-12 10:53:55.512][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2022-04-12 10:53:55.512][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2022-04-12 10:53:55.515][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-04-12 10:53:55.517][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-04-12 10:53:55.520][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2022-04-12 10:53:55.523][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-04-12 10:53:55.526][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-04-12 10:53:55.530][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-04-12 10:53:55.535][super$initialize] Initialize connector chebi.
biodb.DEBUG[2022-04-12 10:53:55.537][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2022-04-12 10:53:55.539][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2022-04-12 10:53:55.541][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2022-04-12 10:53:55.542][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:55.545][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-04-12 10:53:55.547][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2022-04-12 10:53:55.549][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2022-04-12 10:53:55.552][biodb::testThat]
biodb.INFO [2022-04-12 10:53:55.553][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2022-04-12 10:53:55.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-04-12 10:53:55.555][biodb::testThat]
biodb.DEBUG[2022-04-12 10:53:55.560][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2022-04-12 10:53:55.565][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:55.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2022-04-12 10:53:55.569][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:55.570][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2022-04-12 10:53:55.574][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2022-04-12 10:53:55.580][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-04-12 10:53:55.582][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2022-04-12 10:53:55.583][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-04-12 10:53:55.585][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2022-04-12 10:53:55.590][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2022-04-12 10:53:55.592][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2022-04-12 10:53:55.594][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2022-04-12 10:53:55.596][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-04-12 10:53:55.598][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-04-12 10:53:55.600][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2022-04-12 10:53:55.602][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2022-04-12 10:53:55.603][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-04-12 10:53:55.604][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-04-12 10:53:55.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:55.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:55.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:55.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:55.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:55.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:55.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-04-12 10:53:55.622][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2022-04-12 10:53:55.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-04-12 10:53:55.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-04-12 10:53:55.630][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2022-04-12 10:53:56.185][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2022-04-12 10:53:57.050][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-04-12 10:53:57.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2022-04-12 10:53:57.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2022-04-12 10:53:57.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2022-04-12 10:53:57.221][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-04-12 10:53:57.270][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2022-04-12 10:53:57.272][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2022-04-12 10:53:57.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-04-12 10:53:57.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:57.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:57.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:57.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:57.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:57.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-04-12 10:53:57.290][ef$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.293][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.294][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.322][ef$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:57.324][ef$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:57.326][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.328][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.330][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2022-04-12 10:53:57.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2022-04-12 10:53:57.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.353][ef$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:57.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:57.356][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.358][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-04-12 10:53:57.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-04-12 10:53:57.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.386][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-04-12 10:53:57.388][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-04-12 10:53:57.390][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.392][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.395][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-04-12 10:53:57.397][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-04-12 10:53:57.399][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.401][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.403][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:57.405][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:57.407][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.409][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.411][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-04-12 10:53:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.435][ef$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:57.437][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:57.439][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.441][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2022-04-12 10:53:57.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-04-12 10:53:57.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:57.468][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:57.470][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.472][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:57.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-04-12 10:53:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.502][ef$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:57.504][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:57.506][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.508][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-04-12 10:53:57.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-04-12 10:53:57.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.533][ef$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:57.534][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:57.536][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.538][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2022-04-12 10:53:57.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2022-04-12 10:53:57.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.567][ef$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:57.570][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:57.571][ef$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.573][ef$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2022-04-12 10:53:57.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2022-04-12 10:53:57.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-04-12 10:53:57.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-04-12 10:53:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-04-12 10:53:57.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-04-12 10:53:57.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-04-12 10:53:57.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-04-12 10:53:57.690][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2022-04-12 10:53:57.693][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-04-12 10:53:57.695][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2022-04-12 10:53:57.697][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2022-04-12 10:53:57.699][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-04-12 10:53:57.700][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-04-12 10:53:57.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-04-12 10:53:57.704][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-04-12 10:53:57.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-04-12 10:53:57.707][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-04-12 10:53:57.709][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 355 ]
>
> proc.time()
user system elapsed
40.773 1.199 81.744
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.335 | 0.626 | 5.950 | |
| ChebiEntry | 0.853 | 0.018 | 0.874 | |