Pierrick Roger
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: devel |
| git_last_commit: 686a27c |
| git_last_commit_date: 2024-10-29 11:04:36 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 200/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.13.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz |
| StartedAt: 2024-11-27 20:01:37 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 20:09:58 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 501.6 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 2.742 1.85 56.404
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-11-27 20:08:31.901][biodb::testContext]
biodb.INFO [2024-11-27 20:08:31.916][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:08:31.917][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-27 20:08:31.919][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:08:31.920][biodb::testContext]
biodb.INFO [2024-11-27 20:08:31.948][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:08:31.952][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:08:31.975][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:08:31.977][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:08:31.978][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:08:31.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:31.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:31.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:31.982][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:08:31.999][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:08:32.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.003][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[2024-11-27 20:08:32.005][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:08:32.006][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:08:32.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.011][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:08:32.012][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:08:32.013][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:08:32.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.020][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:08:32.022][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:08:32.023][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:08:32.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.026][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:08:32.028][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:08:32.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.032][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:08:32.033][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:08:32.035][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:08:32.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.039][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:08:32.040][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:08:32.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.044][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:08:32.045][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:08:32.047][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:08:32.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.051][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:08:32.052][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:08:32.052][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:08:32.054][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:08:32.055][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:08:32.056][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:08:32.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.061][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:08:32.062][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:08:32.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.077][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:08:32.079][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:08:32.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.082][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[2024-11-27 20:08:32.084][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:08:32.085][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:08:32.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.090][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:08:32.091][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:08:32.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.095][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:08:32.096][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:08:32.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.101][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:08:32.102][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:08:32.220][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:08:32.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.233][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:08:32.234][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:08:32.235][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:08:32.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.245][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:08:32.294][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.315][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:08:32.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:08:32.320][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.322][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.323][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.324][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:08:32.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:08:32.336][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.337][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:08:32.338][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:08:32.340][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.343][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:08:32.343][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:08:32.343][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:08:32.343][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:08:32.343][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:08:32.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:08:32.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.348][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:08:32.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.352][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.368][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:08:32.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:08:32.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.372][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.374][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:08:32.376][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.377][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:08:32.378][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:08:32.381][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.383][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.384][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.386][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:08:32.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:08:32.389][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.391][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:08:32.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:08:32.394][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.396][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.398][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:08:32.398][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:08:32.398][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:08:32.398][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:08:32.398][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:08:32.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:08:32.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.402][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:08:32.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.406][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.407][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.408][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:08:32.409][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:08:32.410][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.412][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.413][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:08:32.416][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.417][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:08:32.418][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.419][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:08:32.420][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.424][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.425][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:08:32.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:08:32.428][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.429][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:08:32.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:08:32.432][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.434][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:08:32.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:08:32.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.442][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.443][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:08:32.444][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:08:32.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.446][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.447][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:08:32.469][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:08:32.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.474][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:08:32.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.476][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.477][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.479][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:08:32.479][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:08:32.480][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.481][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:08:32.482][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:08:32.483][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.484][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.485][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.486][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:08:32.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:08:32.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.492][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:08:32.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:08:32.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.495][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:08:32.499][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:08:32.500][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.615][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[2024-11-27 20:08:32.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.632][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:08:32.638][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:08:32.639][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:08:32.641][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:08:32.643][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:08:32.644][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:08:32.646][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:08:32.647][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:08:32.650][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:08:32.651][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:08:32.653][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:08:32.654][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:08:32.656][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:08:32.658][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:08:32.660][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:08:32.661][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:08:32.663][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:08:32.664][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:08:32.666][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:08:32.667][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:08:32.669][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:08:32.671][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:08:32.673][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:08:32.674][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:08:32.675][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:08:32.676][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:08:32.678][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:08:32.679][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:08:32.681][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:08:32.682][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:08:32.684][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:08:32.685][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:08:32.686][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:08:32.688][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:08:32.690][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:08:32.691][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:08:32.693][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:08:32.694][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:08:32.695][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:08:32.697][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:08:32.699][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:08:32.701][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:08:32.703][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:08:32.704][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:08:32.706][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:08:32.707][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:08:32.710][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:08:32.712][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:08:32.713][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:08:32.715][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:08:32.718][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:08:32.719][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:08:32.721][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:08:32.723][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:08:32.724][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:08:32.726][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:08:32.729][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:08:32.730][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:08:32.732][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:08:32.734][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:08:32.736][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:08:32.738][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:08:32.739][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:08:32.741][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:08:32.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:08:32.745][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:08:32.747][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:08:32.750][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:08:32.751][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:08:32.753][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:08:32.755][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:08:32.757][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:08:32.759][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:08:32.760][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:08:32.762][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:08:32.764][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:08:32.765][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:08:32.767][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:08:32.768][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:08:32.770][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:08:32.772][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:08:32.774][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:08:32.775][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:08:32.783][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:08:32.785][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:08:32.790][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:08:32.791][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.793][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:08:32.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:32.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:32.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:32.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:32.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:32.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:32.931][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:08:32.943][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:08:32.946][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.947][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:08:32.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.954][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.955][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:08:32.956][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:08:32.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:08:32.958][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.959][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:08:32.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:08:32.961][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:08:32.962][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:08:32.963][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:08:32.963][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:08:32.963][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:08:32.964][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:08:32.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:08:32.969][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:08:32.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:08:32.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:08:32.972][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:32.972][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:08:32.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:08:32.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:08:32.976][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:08:32.977][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:08:32.977][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:08:32.983][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:08:32.985][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:08:32.986][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:08:32.988][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:08:32.990][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:08:32.991][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:08:33.020][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:08:33.021][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:08:33.027][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:08:33.032][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:08:33.037][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:08:33.038][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:08:33.039][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:08:33.040][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:08:33.052][biodb::testThat]
biodb.INFO [2024-11-27 20:08:33.054][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-27 20:08:33.055][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:33.057][biodb::testThat]
biodb.TRACE[2024-11-27 20:08:33.074][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-27 20:08:33.076][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:33.080][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:33.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:33.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:33.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:33.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:33.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:33.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:33.233][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.TRACE[2024-11-27 20:08:33.246][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.250][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.271][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.273][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.307][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.313][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.315][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.317][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.324][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:33.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:33.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.328][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:33.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:33.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.334][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.336][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.338][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.344][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:33.345][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:33.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.349][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.354][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:33.355][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:33.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.363][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.367][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.372][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.375][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.380][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:33.381][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.383][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.388][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:33.389][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:33.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.399][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:33.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:33.474][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-27 20:08:33.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:33.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:33.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:33.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:33.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:33.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:33.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:33.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.531][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:33.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:33.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:33.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:33.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:33.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.657][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.658][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.660][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:33.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:33.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.692][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.694][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.696][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:33.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.734][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.831][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:33.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:33.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.860][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.861][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.863][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:33.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.887][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.888][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.890][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.920][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.921][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.923][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.938][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.943][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.950][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.951][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.954][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.955][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:33.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:33.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.977][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.980][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.983][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.984][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.986][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:33.987][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:33.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:33.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.005][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.014][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.016][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.019][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.034][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.045][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.051][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.053][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.085][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.087][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.119][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.136][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.137][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.139][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.145][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:34.147][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:34.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.149][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.162][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:34.164][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:34.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.167][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.174][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.175][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.178][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.185][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.190][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.196][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.198][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.200][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.208][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:34.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:34.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.218][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.219][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.221][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.229][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-27 20:08:34.231][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:34.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.241][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.242][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.244][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.253][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:08:34.265][biodb::testThat]
biodb.INFO [2024-11-27 20:08:34.266][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-27 20:08:34.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:34.269][biodb::testThat]
biodb.DEBUG[2024-11-27 20:08:34.287][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-27 20:08:34.295][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:34.298][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-27 20:08:34.300][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:34.302][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-27 20:08:34.303][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:34.332][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:34.333][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:34.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:34.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:34.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:34.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:34.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:34.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:34.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:34.358][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.361][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.385][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:34.387][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:34.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.390][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.391][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:34.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:34.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.396][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:34.397][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:34.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.399][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:34.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:34.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.406][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.407][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.409][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:34.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:34.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.416][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.419][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:34.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.426][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.430][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.431][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:34.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.435][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:34.437][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:34.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.439][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.440][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:34.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:34.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.446][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.447][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.449][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:34.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.456][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.457][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.459][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.466][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:34.467][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:34.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.469][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.471][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:34.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:34.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.476][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.477][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.482][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:34.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:34.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:34.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:34.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:34.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:34.536][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-27 20:08:34.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-27 20:08:34.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-27 20:08:34.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-27 20:08:34.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-27 20:08:34.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-27 20:08:34.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-27 20:08:34.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:08:34.563][biodb::testThat]
biodb.INFO [2024-11-27 20:08:34.564][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-27 20:08:34.566][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:34.567][biodb::testThat]
biodb.TRACE[2024-11-27 20:08:34.571][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.572][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.574][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:34.576][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-27 20:08:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:34.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:34.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:34.627][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-27 20:08:34.631][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:08:34.655][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:08:34.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:08:34.676][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:34.684][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:08:34.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:34.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:34.713][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:34.715][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:08:35.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:08:35.887][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:35.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-27 20:08:35.908][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-27 20:08:35.922][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-27 20:08:35.939][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:35.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:35.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:35.943][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:35.944][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:35.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:35.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:35.948][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:08:35.956][biodb::testThat]
biodb.INFO [2024-11-27 20:08:35.958][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-27 20:08:35.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:35.960][biodb::testThat]
biodb.TRACE[2024-11-27 20:08:35.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:35.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:36.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:36.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:36.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:36.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:36.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:36.098][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:36.102][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:08:36.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:08:36.105][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:36.108][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-27 20:08:36.133][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.134][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-27 20:08:36.135][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:36.136][biodb::testThat]
biodb.TRACE[2024-11-27 20:08:36.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:36.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:36.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:36.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.197][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:36.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:36.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:36.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:36.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:36.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:36.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:36.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:36.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:36.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-27 20:08:36.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:36.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-27 20:08:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:36.258][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:36.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-27 20:08:36.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:36.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:08:36.268][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.269][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-27 20:08:36.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:36.271][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.285][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.287][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-27 20:08:36.288][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:36.289][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.300][biodb::testThat]
biodb.INFO [2024-11-27 20:08:36.301][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-27 20:08:36.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:36.303][biodb::testThat]
biodb.DEBUG[2024-11-27 20:08:36.308][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-27 20:08:37.022][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-27 20:08:38.321][biodb::testThat]
biodb.INFO [2024-11-27 20:08:38.322][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-27 20:08:38.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:38.324][biodb::testThat]
biodb.DEBUG[2024-11-27 20:08:38.749][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-11-27 20:08:39.168][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:39.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:39.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.171][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.172][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:39.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:39.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.175][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:08:39.177][biodb::testThat]
biodb.INFO [2024-11-27 20:08:39.178][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-27 20:08:39.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:08:39.180][biodb::testThat]
biodb.TRACE[2024-11-27 20:08:39.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:39.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:39.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:39.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:39.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:39.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:39.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:08:39.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:08:39.334][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:39.336][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:08:39.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:39.412][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:08:39.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:08:39.415][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:39.417][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-27 20:08:39.438][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:08:39.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:08:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:39.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:39.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:39.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:39.486][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:39.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:39.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:39.527][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:08:39.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:08:40.219][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:40.221][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-27 20:08:40.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-27 20:08:40.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:40.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:40.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:40.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:40.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:40.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:40.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:40.238][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-27 20:08:40.283][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:40.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-27 20:08:40.286][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:40.287][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:40.288][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:40.289][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:40.290][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:40.290][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:40.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:40.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:40.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:40.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:40.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:40.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:40.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:40.304][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-27 20:08:40.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:40.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:40.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-27 20:08:40.910][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-27 20:08:41.264][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:41.266][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-27 20:08:41.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-27 20:08:41.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-27 20:08:41.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:41.276][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:41.277][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:41.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:41.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:41.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:41.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:41.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:41.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:41.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:41.295][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.296][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.298][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.302][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:41.303][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:41.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.309][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:41.310][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:41.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.325][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:41.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:41.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:41.330][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:41.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:41.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.337][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:41.338][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:41.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:41.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.362][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:41.363][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:41.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.365][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.366][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:41.367][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.369][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:41.375][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:41.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.378][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:41.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.384][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:41.384][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:41.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.386][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:41.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:41.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.392][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:41.393][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:41.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.394][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.395][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:41.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:41.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.399][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:41.400][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:41.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.402][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:41.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:41.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:41.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:41.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:41.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:41.506][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-27 20:08:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:41.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:41.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:41.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:41.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:41.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:41.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:41.535][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:08:41.889][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:08:42.233][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:42.235][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-27 20:08:42.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-27 20:08:42.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:42.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:42.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:42.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:42.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:42.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:42.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:42.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:42.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:42.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:42.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:42.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:42.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:42.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:42.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:42.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:42.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:42.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:42.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:42.285][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-27 20:08:42.286][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:42.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-27 20:08:42.289][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:42.290][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:42.291][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:42.299][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:42.300][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:42.300][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:42.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:42.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:42.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:42.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:42.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:42.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:42.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:42.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-27 20:08:42.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:42.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:42.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-27 20:08:42.670][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-27 20:08:43.045][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:43.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-27 20:08:43.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-27 20:08:43.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-27 20:08:43.054][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:43.055][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:43.056][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:43.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:43.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:43.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:43.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:43.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:43.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:43.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:43.069][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.070][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.071][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.076][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:43.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:43.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.078][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:43.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:43.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.093][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:43.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:43.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.096][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:43.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:43.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:43.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:43.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:43.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:43.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.129][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:43.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:43.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.144][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:43.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:43.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.149][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:43.150][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:43.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.152][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.154][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:43.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.157][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:43.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.163][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:43.163][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:43.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.165][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:43.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:43.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.170][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:43.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:43.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.172][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:43.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:43.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.178][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:43.179][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:43.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.181][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.182][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:43.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:43.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.186][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:43.188][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:43.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.190][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.192][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:43.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:43.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:43.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:43.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:43.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:43.240][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-27 20:08:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:43.313][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:08:43.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:08:43.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:08:43.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:08:43.320][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:08:43.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:43.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:43.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:43.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:43.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:43.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:43.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:43.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:43.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:43.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:43.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:43.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:43.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:43.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:43.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:43.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:43.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:43.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:43.356][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-27 20:08:43.357][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:43.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-27 20:08:43.360][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:43.361][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:43.362][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:43.363][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:43.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:43.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:43.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:43.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:43.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:43.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:43.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:43.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:43.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:43.381][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-27 20:08:43.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:43.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:43.386][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-27 20:08:43.739][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-27 20:08:44.093][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:44.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-27 20:08:44.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-27 20:08:44.101][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-27 20:08:44.103][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:44.104][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:44.105][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:44.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:44.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:44.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:44.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:44.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:44.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:44.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:44.120][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.122][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.123][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.128][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:44.129][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:44.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.130][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:44.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:44.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.134][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.135][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:44.136][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:44.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.138][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.139][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:44.140][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:44.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.141][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.142][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:44.143][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:44.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.145][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.146][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:44.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.149][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.151][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:44.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:44.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.154][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:44.156][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:44.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.159][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:44.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.163][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:44.164][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:44.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.166][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.174][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:44.175][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:44.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.177][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:44.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:44.219][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-27 20:08:44.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:44.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:44.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:44.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:44.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:44.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:44.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:44.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:44.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:44.250][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-27 20:08:44.251][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:44.253][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-27 20:08:44.255][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:44.256][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:44.257][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:44.258][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:44.259][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:44.259][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:44.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:44.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:44.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:44.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:44.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:44.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:44.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:44.272][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-27 20:08:44.274][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:44.275][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:44.276][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-27 20:08:44.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-27 20:08:44.956][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:44.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-27 20:08:44.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-27 20:08:44.964][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-27 20:08:44.966][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:44.967][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:44.976][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:44.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:44.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:44.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:44.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:44.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:44.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:44.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:44.988][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.990][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:44.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:44.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.994][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:44.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:44.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:44.997][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:44.998][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:44.998][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:44.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.000][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:45.002][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:45.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.003][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.005][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:45.005][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:45.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.007][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.008][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:45.009][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:45.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.010][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.011][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:45.012][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.013][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.014][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:45.015][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:45.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.017][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:45.018][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:45.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.020][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.024][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:45.025][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:45.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.026][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.030][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:45.031][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:45.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.033][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:45.074][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-27 20:08:45.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:45.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:45.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:45.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:45.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:45.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:45.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:45.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:45.104][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-27 20:08:45.105][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:45.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-27 20:08:45.111][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:45.112][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:45.113][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:45.114][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:45.114][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:45.115][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:45.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:45.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:45.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:45.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:45.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:45.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:45.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:45.129][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-27 20:08:45.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:45.132][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:45.133][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-27 20:08:45.478][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-27 20:08:45.823][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:45.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-27 20:08:45.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-27 20:08:45.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-27 20:08:45.831][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:45.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:45.833][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:45.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:45.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:45.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:45.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:45.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:45.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:45.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:45.853][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.855][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.860][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:45.860][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:45.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.862][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.863][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:45.864][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:45.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:45.867][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:45.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.869][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.870][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:45.870][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:45.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.872][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.873][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:45.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:45.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.875][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.876][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:45.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.879][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:45.880][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:45.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.882][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.883][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:45.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:45.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.885][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:45.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:45.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.889][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:45.890][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:45.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.892][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.893][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.907][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:45.908][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:45.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.909][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:45.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:45.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:45.959][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-27 20:08:45.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:45.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:45.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:45.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:45.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:45.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:45.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:45.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:45.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:45.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:45.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:45.986][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-27 20:08:45.987][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:45.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-27 20:08:45.993][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:45.994][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:45.995][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:45.995][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:45.996][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:45.997][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:46.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:46.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:46.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:46.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:46.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:46.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:46.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:46.011][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-27 20:08:46.013][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:46.014][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:46.015][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-27 20:08:46.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-27 20:08:46.920][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:46.922][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-27 20:08:46.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-27 20:08:46.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-27 20:08:46.928][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:46.929][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:46.930][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:46.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:46.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:46.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:46.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:46.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:46.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:46.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:46.942][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:46.943][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:46.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.945][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:46.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:46.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.957][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:46.958][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:46.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.960][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:46.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:46.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.964][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:46.965][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:46.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.966][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.967][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:46.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:46.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.971][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:46.971][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:46.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.973][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:46.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:46.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:46.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:46.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.980][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:46.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:46.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:46.986][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:46.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.987][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.988][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:46.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:46.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.992][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:46.992][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:46.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.994][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.995][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:46.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:46.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:46.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:46.998][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:46.999][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.001][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:47.006][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:47.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.015][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:47.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:47.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.020][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:47.021][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:47.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.022][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:47.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:47.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.026][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:47.027][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:47.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.029][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:47.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:47.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:47.070][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-27 20:08:47.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:47.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:47.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:47.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:47.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:47.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:47.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:47.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:47.089][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-27 20:08:47.090][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:47.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-27 20:08:47.093][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:47.093][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:47.094][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:47.095][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:47.096][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:47.097][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:47.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:47.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:47.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:47.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:47.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:47.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:47.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:47.108][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-27 20:08:47.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:47.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:47.112][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-27 20:08:47.482][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-27 20:08:47.825][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:47.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-27 20:08:47.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-27 20:08:47.834][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-27 20:08:47.836][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:47.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:47.839][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:47.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:47.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:47.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:47.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:47.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:47.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:47.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:47.868][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.870][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.873][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.878][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:47.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:47.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.881][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.882][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:47.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:47.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.886][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:47.887][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:47.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.889][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:47.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:47.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.893][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:47.894][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:47.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.896][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:47.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.901][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:47.901][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:47.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.903][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:47.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:47.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.908][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:47.909][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:47.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.912][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.913][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:47.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:47.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.917][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:47.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.920][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:47.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.924][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.925][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.926][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:47.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.931][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:47.932][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:47.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.934][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:47.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:47.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.938][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:47.939][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:47.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.941][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.942][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:47.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:47.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.945][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:47.946][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:47.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.948][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.949][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:47.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:47.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:47.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:47.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:47.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:47.993][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-27 20:08:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:47.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:47.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:47.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:48.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:48.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:48.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:48.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:48.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:48.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:48.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:48.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:48.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:48.015][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-27 20:08:48.016][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:48.017][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-27 20:08:48.018][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:48.019][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:48.020][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:48.021][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:48.022][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:48.023][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:48.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:48.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:48.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:48.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:48.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:48.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:48.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:48.035][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-27 20:08:48.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:48.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:48.040][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-27 20:08:48.387][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-27 20:08:48.864][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:48.867][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-27 20:08:48.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-27 20:08:48.874][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-27 20:08:48.877][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:48.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:48.880][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:48.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:48.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:48.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:48.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:48.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:48.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:48.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:48.899][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:48.901][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:48.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.903][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:48.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:48.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.910][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:48.911][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:48.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.915][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:48.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:48.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.919][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:48.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:48.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.923][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:48.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:48.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.930][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:48.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:48.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.933][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:48.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.939][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:48.940][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:48.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:48.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:48.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.949][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:48.950][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:48.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.952][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.954][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:48.955][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:48.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.958][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.959][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.965][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:48.966][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:48.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.969][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:48.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:48.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.976][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:48.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:48.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.980][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:48.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:48.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:48.987][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:48.988][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:48.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:48.998][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:49.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:49.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.006][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:49.007][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:49.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.010][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.011][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:49.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:49.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:49.060][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-27 20:08:49.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:49.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:49.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:49.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:49.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:49.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:49.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:49.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:49.084][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-27 20:08:49.085][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:49.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-27 20:08:49.088][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:49.089][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:49.090][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:49.091][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:49.093][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:49.093][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:49.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:49.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:49.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:49.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:49.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:49.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:49.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:49.114][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-27 20:08:49.116][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:49.117][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:49.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-27 20:08:49.471][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-27 20:08:49.826][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:49.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-27 20:08:49.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-27 20:08:49.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-27 20:08:49.836][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:49.837][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:49.838][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:49.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:49.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:49.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:49.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:49.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:49.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:49.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:49.867][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.868][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.870][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.874][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:49.875][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:49.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.877][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.878][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:49.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:49.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.881][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:49.882][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:49.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.884][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:49.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:49.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.888][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:49.889][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:49.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:49.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:49.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.896][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:49.897][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:49.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.898][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:49.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.903][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:49.904][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:49.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.929][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.931][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:49.932][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.933][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.935][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:49.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.938][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:49.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:49.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.940][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:49.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:49.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.952][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:49.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:49.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.955][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:49.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:49.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.959][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:49.960][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:49.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.962][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:49.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:49.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.968][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:49.969][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:49.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.971][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.973][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:49.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:49.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:49.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:49.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:49.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:50.014][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-27 20:08:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:50.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:50.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:50.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:50.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:50.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:50.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:50.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:50.035][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-27 20:08:50.036][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:50.038][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-27 20:08:50.039][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:50.040][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:50.045][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:50.046][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:50.047][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:50.048][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:50.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:50.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:50.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:50.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:50.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:50.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:50.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:50.070][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-27 20:08:50.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:50.073][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:50.074][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-27 20:08:50.471][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-27 20:08:50.814][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:50.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-27 20:08:50.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-27 20:08:50.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-27 20:08:50.824][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:50.825][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:50.826][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:50.827][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:50.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:50.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:50.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:50.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:50.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:50.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:50.842][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.845][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.849][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:50.850][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:50.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.852][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.853][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:50.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:50.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.857][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:50.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:50.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.859][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:50.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:50.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:50.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:50.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.866][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:50.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:50.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.870][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:50.871][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:50.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.872][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:50.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:50.878][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:50.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.879][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.880][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:50.881][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.892][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:50.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:50.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.898][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:50.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:50.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.903][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:50.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:50.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.905][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:50.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.910][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:50.911][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:50.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.914][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.917][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:50.918][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:50.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.919][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.921][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:50.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:50.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:50.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:50.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:50.959][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-27 20:08:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:50.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:50.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:50.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:50.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:50.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:50.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:50.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:50.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:50.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:50.988][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-27 20:08:50.989][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:50.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-27 20:08:50.992][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:50.993][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:50.994][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:50.994][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:50.995][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:50.996][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:50.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:51.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:51.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:51.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:51.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:51.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:51.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:51.009][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-27 20:08:51.011][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:51.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:51.013][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-27 20:08:51.366][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-27 20:08:51.713][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:51.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-27 20:08:51.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-27 20:08:51.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-27 20:08:51.722][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:51.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:51.724][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:51.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:51.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:51.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:51.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:51.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:51.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:51.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:51.738][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.739][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.741][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:51.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:51.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.748][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.752][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:51.753][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:51.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:51.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:51.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:51.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:51.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.762][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:51.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:51.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.766][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:51.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:51.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.777][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:51.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:51.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.782][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:51.783][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:51.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.784][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.786][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:51.786][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.788][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.792][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:51.793][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:51.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.795][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:51.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:51.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.799][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:51.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:51.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:51.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:51.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.807][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:51.808][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:51.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.810][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.811][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:51.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:51.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.815][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:51.815][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:51.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.817][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.818][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:51.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:51.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:51.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:51.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:51.858][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-27 20:08:51.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:51.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:51.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:51.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:51.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:51.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:51.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:51.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:51.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:51.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:51.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:51.886][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-27 20:08:51.886][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:51.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.INFO [2024-11-27 20:08:51.907][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-27 20:08:51.928][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:51.930][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:51.931][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:51.932][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:51.933][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:51.933][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:51.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:51.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:51.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:51.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:51.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:51.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:51.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:51.970][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-27 20:08:51.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:51.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:51.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-27 20:08:52.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-27 20:08:52.681][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:52.683][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-27 20:08:52.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-27 20:08:52.688][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-27 20:08:52.690][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:52.691][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:52.692][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:52.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:52.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:52.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:52.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:52.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:52.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:52.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:52.704][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.705][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.707][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.711][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:52.712][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:52.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.714][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.715][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:52.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.718][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:52.719][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:52.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.728][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:52.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.737][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:52.738][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:52.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.741][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:52.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:52.748][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:52.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.750][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.751][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:52.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:52.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.754][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:52.755][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:52.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.757][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.758][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:52.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.760][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:52.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.765][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:52.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:52.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.768][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:52.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.772][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:52.773][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:52.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.774][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:52.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:52.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:52.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:52.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.782][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.783][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:52.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:52.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.786][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:52.787][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:52.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.789][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.790][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:52.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:52.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:52.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:52.835][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-27 20:08:52.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:52.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:52.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:52.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:52.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:52.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:52.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:52.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:52.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:52.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:52.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:52.855][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-27 20:08:52.856][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:52.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-27 20:08:52.858][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:52.859][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:52.860][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:52.861][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:52.862][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:52.863][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:52.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:52.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:52.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:52.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:52.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:52.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:52.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:52.874][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-27 20:08:52.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:52.878][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:52.879][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-27 20:08:53.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-27 20:08:53.582][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:53.584][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-27 20:08:53.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-27 20:08:53.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-27 20:08:53.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:53.592][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:53.593][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:53.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:53.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:53.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:53.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:53.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:53.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:53.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:53.606][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.608][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.621][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:53.622][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:53.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.623][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.628][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:53.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:53.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.630][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.635][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:53.636][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:53.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.637][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.638][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:53.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:53.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.641][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.642][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:53.643][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:53.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.644][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.645][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:53.646][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.648][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.649][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:53.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.652][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:53.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:53.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.655][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:53.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.660][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:53.660][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:53.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.662][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.667][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:53.668][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:53.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.669][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.670][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:53.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:53.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.674][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:53.675][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:53.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.676][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:53.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:53.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:53.715][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-27 20:08:53.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:53.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:53.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:53.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:53.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:53.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:53.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:53.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:53.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:53.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:53.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:53.735][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-27 20:08:53.736][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:53.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-27 20:08:53.738][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:53.739][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:53.740][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:53.741][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:53.742][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:53.743][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:53.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:53.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:53.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:53.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:53.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:53.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:53.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:53.754][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-11-27 20:08:53.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:53.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:53.759][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-11-27 20:08:54.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-11-27 20:08:54.459][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:54.523][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-11-27 20:08:54.526][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-11-27 20:08:54.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-11-27 20:08:54.530][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:54.531][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:54.532][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:54.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:54.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:54.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:54.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:54.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:54.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:54.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:54.555][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.557][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.570][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:54.571][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:54.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.573][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.574][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:54.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.578][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:54.578][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:54.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.580][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.584][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:54.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:54.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.588][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:54.589][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:54.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.591][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.592][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:54.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:54.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.594][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.595][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:54.596][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.598][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.599][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:54.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.602][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:54.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:54.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.605][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:54.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:54.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.609][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:54.610][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:54.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.612][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:54.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.617][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:54.618][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:54.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.619][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:54.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:54.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.624][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:54.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:54.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.626][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:54.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:54.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:54.669][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-27 20:08:54.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:54.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:54.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:54.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:54.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:54.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:54.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:54.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:54.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:54.762][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-27 20:08:54.762][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:54.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.INFO [2024-11-27 20:08:54.765][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-27 20:08:54.766][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:54.767][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:54.768][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:54.769][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:54.770][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:54.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:54.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:54.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:54.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:54.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:54.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:54.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:54.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:54.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-11-27 20:08:54.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:54.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:54.787][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-11-27 20:08:55.152][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-11-27 20:08:55.493][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:55.495][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-11-27 20:08:55.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-11-27 20:08:55.501][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-11-27 20:08:55.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:55.503][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:55.504][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:55.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:55.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:55.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:55.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:55.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:55.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:55.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:55.517][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.517][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.533][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:55.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:55.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.536][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.537][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:55.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:55.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.541][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:55.541][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:55.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.543][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:55.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:55.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.547][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:55.548][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:55.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:55.555][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:55.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.557][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:55.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:55.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.561][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:55.562][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:55.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.564][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.565][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:55.566][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.567][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.568][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:55.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.572][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:55.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:55.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.574][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:55.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:55.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.579][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:55.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:55.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.581][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:55.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:55.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.586][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:55.587][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:55.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.588][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:55.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:55.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.593][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:55.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:55.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:55.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:55.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:55.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:55.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:55.638][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-27 20:08:55.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:55.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:55.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:55.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:55.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:55.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:55.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:55.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:55.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:55.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:55.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:55.659][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-27 20:08:55.660][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:55.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-27 20:08:55.662][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:55.663][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:55.664][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:55.665][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:55.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:55.666][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:55.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:55.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:55.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:55.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:55.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:55.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:55.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:55.679][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-11-27 20:08:55.681][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:55.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:55.683][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-11-27 20:08:56.045][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-11-27 20:08:56.392][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:56.394][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-11-27 20:08:56.397][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-11-27 20:08:56.399][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-11-27 20:08:56.401][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:56.402][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:56.403][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:56.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:56.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:56.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:56.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:56.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:56.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:56.440][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[2024-11-27 20:08:56.442][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.443][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.445][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.449][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:56.450][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:56.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.452][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.453][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:56.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:56.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.457][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:56.458][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:56.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.460][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:56.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:56.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:56.466][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:56.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.467][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:56.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:56.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.472][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:56.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:56.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.474][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:56.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.479][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:56.480][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:56.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.483][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:56.484][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.485][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:56.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.490][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:56.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:56.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.492][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:56.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.497][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:56.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:56.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.499][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:56.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:56.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.504][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:56.505][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:56.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.506][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.507][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:56.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:56.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.511][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:56.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:56.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:56.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:56.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:56.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:56.565][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-27 20:08:56.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:56.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:56.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:56.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:56.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:56.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:56.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:56.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:56.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:56.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:56.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:56.589][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-27 20:08:56.590][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:56.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-27 20:08:56.592][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:56.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:56.594][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:56.595][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:56.596][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:56.597][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:56.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:56.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:56.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:56.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:56.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:56.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:56.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:56.608][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-11-27 20:08:56.611][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:56.611][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:56.613][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-11-27 20:08:56.971][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-11-27 20:08:57.316][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:57.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-11-27 20:08:57.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-11-27 20:08:57.332][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-11-27 20:08:57.334][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:57.335][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:57.337][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:57.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:57.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:57.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:57.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:57.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:57.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:57.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:57.355][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.358][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.361][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.368][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:57.370][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:57.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:57.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:57.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.388][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:57.401][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:57.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.412][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:57.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.442][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:57.448][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:57.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.457][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:57.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:57.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.469][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:57.472][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:57.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.481][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:57.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:57.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:57.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:57.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.493][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.495][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:57.496][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.498][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.500][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:57.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.505][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:57.506][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:57.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.509][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.529][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:57.534][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:57.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.545][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.565][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:57.567][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:57.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:57.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.600][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:57.602][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:57.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.606][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:57.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:57.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:57.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:57.647][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-27 20:08:57.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:57.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:57.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:57.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:57.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:57.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:57.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:57.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:57.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:57.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:57.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:57.691][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-27 20:08:57.693][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:57.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-27 20:08:57.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:57.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:57.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:57.701][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:57.702][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:57.704][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:57.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:57.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:57.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:57.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:57.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:57.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:57.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:57.740][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-11-27 20:08:57.745][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:57.746][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:57.747][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-11-27 20:08:58.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-11-27 20:08:58.472][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:08:58.474][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-11-27 20:08:59.149][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-11-27 20:08:59.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-11-27 20:08:59.242][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:08:59.243][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:08:59.244][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:08:59.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:59.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:59.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:59.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:59.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:59.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:59.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:08:59.280][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.282][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.285][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.291][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:59.292][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:59.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.295][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.296][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:08:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:08:59.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.301][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:59.303][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:59.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:08:59.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:08:59.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.312][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:59.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:59.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.315][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:08:59.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:08:59.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.320][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:59.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:59.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:08:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:08:59.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.329][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:59.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:08:59.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.335][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:59.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.338][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:08:59.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.342][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:59.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:59.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:59.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:08:59.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.363][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:59.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:59.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.367][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:08:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:08:59.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:59.376][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:59.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.379][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:08:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:08:59.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:59.386][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:59.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.387][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:08:59.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:08:59.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:08:59.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:08:59.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:08:59.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:59.452][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-27 20:08:59.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:08:59.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:08:59.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:08:59.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:08:59.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:59.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:59.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:59.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:59.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:59.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:59.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:59.495][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-27 20:08:59.497][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:08:59.499][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-27 20:08:59.501][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:08:59.507][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:08:59.508][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:08:59.510][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:08:59.511][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:08:59.513][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:08:59.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:08:59.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:08:59.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:08:59.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:08:59.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:08:59.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:08:59.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:08:59.534][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-11-27 20:08:59.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:08:59.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:08:59.542][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-11-27 20:08:59.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-11-27 20:09:00.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:00.250][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-11-27 20:09:00.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-11-27 20:09:00.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-11-27 20:09:00.257][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:00.258][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:00.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:00.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:00.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:00.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:02.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:02.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:02.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:02.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:02.571][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.572][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.574][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.580][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:02.581][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:02.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.583][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:02.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:02.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.588][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:02.590][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:02.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.592][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.593][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:02.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:02.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.598][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:02.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:02.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.603][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:02.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.610][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:02.612][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:02.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.615][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:02.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:02.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.622][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:02.623][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:02.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.627][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.639][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:02.641][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.643][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.645][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:02.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.652][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:02.654][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:02.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.657][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:02.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:02.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.668][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:02.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:02.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.675][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:02.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:02.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.682][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:02.684][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:02.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.687][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.689][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:02.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:02.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.697][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:02.698][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:02.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.705][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:02.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:02.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:02.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:02.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:02.762][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-27 20:09:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:02.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:02.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:02.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:02.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:02.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:02.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:02.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:02.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:02.798][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-27 20:09:02.799][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:02.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-27 20:09:02.803][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:02.804][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:02.805][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:02.806][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:02.809][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:02.810][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:02.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:02.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:02.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:02.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:02.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:02.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:02.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:02.829][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-11-27 20:09:02.831][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:02.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:02.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-11-27 20:09:03.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-11-27 20:09:03.536][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:03.538][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-11-27 20:09:03.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-11-27 20:09:03.543][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-11-27 20:09:03.545][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:03.546][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:03.547][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:03.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:03.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:03.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:03.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:03.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:03.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:03.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:03.558][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.559][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.560][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.565][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:03.566][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:03.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.567][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.568][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:03.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:03.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.571][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:03.572][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:03.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.574][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:03.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:03.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:03.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:03.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.581][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:03.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:03.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.592][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:03.593][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:03.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:03.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:03.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.599][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:03.600][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:03.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.601][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.602][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:03.603][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.604][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.605][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:03.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.608][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:03.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:03.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:03.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:03.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.615][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:03.616][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:03.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.617][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:03.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:03.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.622][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:03.622][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:03.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.624][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.625][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:03.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:03.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.628][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:03.629][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:03.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.630][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:03.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:03.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:03.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:03.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:03.672][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-27 20:09:03.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:03.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:03.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:03.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:03.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:03.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:03.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:03.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:03.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:03.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:03.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:03.691][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-27 20:09:03.691][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:03.693][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-27 20:09:03.694][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:03.695][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:03.695][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:03.696][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:03.697][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:03.698][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:03.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:03.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:03.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:03.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:03.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:03.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:03.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:03.709][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-11-27 20:09:03.712][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:03.712][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:03.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-11-27 20:09:04.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-11-27 20:09:04.413][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:04.415][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-11-27 20:09:04.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-11-27 20:09:04.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-11-27 20:09:04.421][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:04.422][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:04.423][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:04.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:04.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:04.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:04.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:04.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:04.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:04.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:04.435][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.437][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.441][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:04.442][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:04.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.444][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.445][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:04.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.455][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:04.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:04.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.458][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:04.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:04.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.462][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:04.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:04.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.464][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:04.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:04.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.468][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:04.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:04.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.471][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:04.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.475][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:04.476][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:04.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.478][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:04.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.481][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.482][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:04.486][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:04.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.492][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:04.493][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:04.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:04.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.498][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:04.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:04.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.501][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.502][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:04.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.505][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:04.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:04.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.507][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:04.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:04.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:04.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:04.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:04.548][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-27 20:09:04.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:04.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:04.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:04.579][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:04.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:04.581][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:05.155][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:05.752][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:05.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-27 20:09:05.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-27 20:09:05.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:05.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:05.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:05.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:05.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:05.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:05.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:05.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:05.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:05.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:05.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:05.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:05.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:05.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:05.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:05.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:05.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:05.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:05.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:05.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:05.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:05.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:05.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:05.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:05.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:05.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:05.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:05.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:05.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:05.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:05.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:05.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:05.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:05.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:05.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:05.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:05.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:05.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:05.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:05.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:05.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:05.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.034][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.TRACE[2024-11-27 20:09:06.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.151][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[2024-11-27 20:09:06.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.260][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.TRACE[2024-11-27 20:09:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:06.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:06.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:06.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:06.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:06.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:06.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:06.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:06.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:06.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:06.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:06.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:06.370][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:06.371][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:06.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:06.717][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:07.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:07.087][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-11-27 20:09:07.090][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-11-27 20:09:07.093][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:07.095][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:07.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:07.098][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:07.447][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:07.788][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:07.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-11-27 20:09:07.792][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-11-27 20:09:07.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:07.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:07.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:10.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:10.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:10.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:10.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:10.719][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-27 20:09:10.720][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:10.721][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-27 20:09:10.722][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:10.723][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:10.724][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:10.725][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:10.726][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:10.727][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:10.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:10.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:10.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:10.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:10.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:10.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:10.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:10.740][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-11-27 20:09:10.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:10.743][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:10.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-11-27 20:09:11.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-11-27 20:09:11.439][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:11.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-11-27 20:09:11.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-11-27 20:09:11.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-11-27 20:09:11.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:11.451][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:11.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:11.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:11.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:11.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:11.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:11.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:11.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:11.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:11.465][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.467][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.474][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:11.475][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:11.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.478][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:11.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:11.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.481][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:11.482][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:11.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.485][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:11.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:11.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:11.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:11.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:11.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:11.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.495][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:11.496][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:11.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.498][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:11.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:11.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.502][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:11.503][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:11.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.505][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.509][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:11.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:11.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.513][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:11.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:11.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.516][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.517][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.527][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:11.528][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:11.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.531][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:11.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.539][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:11.540][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:11.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.543][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:11.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:11.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.550][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:11.551][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:11.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.553][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.555][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:11.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:11.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:11.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:11.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:11.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:11.619][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-27 20:09:11.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:11.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:11.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:11.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:11.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:11.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:11.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:11.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:11.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:11.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:11.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:11.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:11.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:11.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:11.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:11.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:11.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:11.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:11.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:11.691][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-27 20:09:11.693][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:11.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-27 20:09:11.698][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:11.700][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:11.701][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:11.703][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:11.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:11.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:11.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:11.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:11.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:11.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:11.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:11.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:11.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:11.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-11-27 20:09:11.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:11.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:11.789][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-11-27 20:09:12.144][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-11-27 20:09:12.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:12.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-11-27 20:09:12.496][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-11-27 20:09:12.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-11-27 20:09:12.500][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:12.501][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:12.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:12.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.514][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.517][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.521][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:12.522][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:12.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.523][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.524][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:12.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.528][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:12.529][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:12.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.530][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:12.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:12.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:12.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:12.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.537][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:12.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:12.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.541][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:12.542][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:12.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:12.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:12.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:12.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:12.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.551][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.552][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:12.553][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:12.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.554][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.555][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:12.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:12.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.559][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.560][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.561][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.565][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:12.566][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:12.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.568][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.572][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:12.573][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:12.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.575][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.576][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:12.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:12.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.579][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:12.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:12.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.582][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.583][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:12.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:12.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:12.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:12.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.619][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-27 20:09:12.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:12.653][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:12.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:09:12.655][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:12.656][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:09:12.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.715][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.TRACE[2024-11-27 20:09:12.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.930][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.TRACE[2024-11-27 20:09:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.969][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[2024-11-27 20:09:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:12.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:12.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:12.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:12.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:12.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:12.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:12.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:12.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:12.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:12.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:12.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.009][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.TRACE[2024-11-27 20:09:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.028][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.TRACE[2024-11-27 20:09:13.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.048][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[2024-11-27 20:09:13.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.096][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:13.099][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:13.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-27 20:09:13.101][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:13.102][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-27 20:09:13.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.113][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.TRACE[2024-11-27 20:09:13.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.327][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.TRACE[2024-11-27 20:09:13.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:13.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:13.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.520][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:13.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:13.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:09:13.530][biodb::testThat]
biodb.INFO [2024-11-27 20:09:13.531][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-27 20:09:13.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:13.533][biodb::testThat]
biodb.TRACE[2024-11-27 20:09:13.535][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:09:13.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:09:13.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:13.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:13.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:13.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:13.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:13.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:13.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:13.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:13.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:13.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:13.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:13.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:13.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:13.568][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:13.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:14.257][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:14.259][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-27 20:09:14.264][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-27 20:09:14.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:14.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:14.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:14.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:14.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:14.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:14.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:14.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:14.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:14.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:14.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:14.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:14.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:14.296][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:14.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:14.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:14.304][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:14.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:14.997][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:14.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-27 20:09:15.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-27 20:09:15.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:15.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:15.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.244][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[2024-11-27 20:09:17.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:17.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:17.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:17.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:17.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:17.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:17.277][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:17.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:17.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:17.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:17.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.301][private$selectFields]
biodb.TRACE[2024-11-27 20:09:17.302][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:17.303][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:17.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.308][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.309][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.310][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.313][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.314][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.315][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.318][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.318][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.349][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:09:17.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:17.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:17.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:17.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.381][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.381][private$selectFields]
biodb.TRACE[2024-11-27 20:09:17.383][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:17.384][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:17.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.390][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.394][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.405][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.406][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.407][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.408][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.409][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.410][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:17.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.421][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:17.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:17.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:17.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.432][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[2024-11-27 20:09:17.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.441][private$selectFields]
biodb.TRACE[2024-11-27 20:09:17.441][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:17.442][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:17.443][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.444][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.445][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.447][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.452][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.454][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:17.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.457][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:17.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:17.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.470][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:09:17.471][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:17.472][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:17.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:17.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:17.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:17.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:17.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:17.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:17.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:17.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:17.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:17.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:17.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:17.553][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:17.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:17.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:17.558][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:17.910][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:18.250][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:18.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-11-27 20:09:18.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-11-27 20:09:18.260][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:18.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:18.264][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:18.265][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:18.610][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:18.963][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:18.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-11-27 20:09:18.969][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-11-27 20:09:18.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:18.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:18.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:18.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:18.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:18.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:18.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:18.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:18.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:18.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:18.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:18.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:18.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:18.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:18.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:18.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:18.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:18.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:18.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.050][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:19.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.099][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.100][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.100][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.108][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.110][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.111][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.113][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.114][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.125][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:09:19.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.167][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.168][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.168][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.169][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.172][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.173][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.174][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.175][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.177][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.186][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.189][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.190][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.201][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:19.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.222][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.223][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.231][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.236][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.236][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.247][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:09:19.248][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:19.249][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:19.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:19.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:09:19.265][biodb::testThat]
biodb.INFO [2024-11-27 20:09:19.266][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-27 20:09:19.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:19.268][biodb::testThat]
biodb.TRACE[2024-11-27 20:09:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:09:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:09:19.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:19.305][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:19.309][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:19.310][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-27 20:09:19.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:19.313][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-27 20:09:19.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:19.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:19.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-27 20:09:19.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:19.347][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-27 20:09:19.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.359][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.TRACE[2024-11-27 20:09:19.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.379][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.TRACE[2024-11-27 20:09:19.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:19.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.390][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:19.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.417][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.418][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.419][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.419][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.423][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.424][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.426][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.428][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.430][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.433][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.434][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:09:19.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.473][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.475][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.477][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.479][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.479][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.481][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.484][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.493][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.494][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.498][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.499][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.514][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:19.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.535][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.537][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.538][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.540][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.541][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.542][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.546][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.548][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.549][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.549][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.550][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.553][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.554][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.572][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:09:19.573][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:19.574][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:19.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:19.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:19.646][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:19.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-27 20:09:19.650][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:19.652][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-27 20:09:19.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:19.660][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:19.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-27 20:09:19.666][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:19.668][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-27 20:09:19.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:19.812][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:19.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.846][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.847][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.849][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.851][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.856][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.862][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.863][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.865][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.868][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.870][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.871][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.888][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:09:19.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:19.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:19.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:19.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:19.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:19.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.921][private$selectFields]
biodb.TRACE[2024-11-27 20:09:19.922][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:19.923][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:19.924][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.925][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.927][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.929][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.930][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.932][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.934][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.935][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.944][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:19.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.949][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.950][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:19.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:19.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:19.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:19.963][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:19.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:19.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:19.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.081][private$selectFields]
biodb.TRACE[2024-11-27 20:09:20.082][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:20.083][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:20.085][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.090][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.095][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.096][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.101][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.102][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:20.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.119][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:09:20.120][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:20.122][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:20.422][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:20.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:09:20.441][biodb::testThat]
biodb.INFO [2024-11-27 20:09:20.443][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-27 20:09:20.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:20.447][biodb::testThat]
biodb.TRACE[2024-11-27 20:09:20.454][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-27 20:09:20.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-27 20:09:20.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:20.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:20.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:20.510][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-27 20:09:20.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:20.514][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-27 20:09:20.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.551][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:20.556][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:20.557][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-27 20:09:20.560][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:20.562][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-27 20:09:20.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.633][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:20.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.665][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.666][private$selectFields]
biodb.TRACE[2024-11-27 20:09:20.667][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:20.669][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:20.670][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.671][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.676][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.681][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.683][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.684][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.687][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.689][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.691][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.709][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-27 20:09:20.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.739][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.741][private$selectFields]
biodb.TRACE[2024-11-27 20:09:20.742][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:20.743][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:20.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.746][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.751][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.752][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.756][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.757][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.760][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.761][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.777][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:20.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.805][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.807][private$selectFields]
biodb.TRACE[2024-11-27 20:09:20.809][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:20.810][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:20.812][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.814][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.815][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.817][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.818][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.819][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.821][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.823][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.824][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:20.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.835][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.836][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:20.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:20.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.853][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-27 20:09:20.854][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:20.855][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:20.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:20.932][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:20.936][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:20.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-27 20:09:20.938][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:20.940][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-27 20:09:20.943][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:20.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:20.949][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-27 20:09:20.951][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:20.952][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-27 20:09:20.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:20.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:20.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:20.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:20.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:20.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:20.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:20.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:20.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:20.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:20.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.006][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.TRACE[2024-11-27 20:09:21.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:21.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:21.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:21.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:21.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:21.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:21.053][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-27 20:09:21.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:21.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:21.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.071][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.TRACE[2024-11-27 20:09:21.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.085][private$selectFields]
biodb.TRACE[2024-11-27 20:09:21.086][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:21.087][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:21.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.092][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.097][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.098][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.100][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.102][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.105][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:21.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.118][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-27 20:09:21.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:21.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:21.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:21.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.144][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.145][private$selectFields]
biodb.TRACE[2024-11-27 20:09:21.146][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:21.146][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:21.147][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.148][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.151][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.156][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.158][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.160][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.162][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.164][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.166][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:21.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.183][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-27 20:09:21.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:21.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:21.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:21.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.207][private$selectFields]
biodb.TRACE[2024-11-27 20:09:21.208][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-27 20:09:21.208][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-27 20:09:21.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.210][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.213][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.220][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-27 20:09:21.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.224][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-27 20:09:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:21.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:21.238][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-27 20:09:21.238][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-27 20:09:21.239][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-27 20:09:21.270][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:21.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-27 20:09:21.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:21.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-27 20:09:21.280][biodb::testThat]
biodb.INFO [2024-11-27 20:09:21.281][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-27 20:09:21.282][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:21.283][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:21.285][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-27 20:09:21.286][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:21.287][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-27 20:09:21.288][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:21.290][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:21.291][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:21.292][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:21.293][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:21.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:21.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:21.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:21.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:21.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:21.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:21.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:21.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:21.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-11-27 20:09:21.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:21.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:21.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-11-27 20:09:21.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-11-27 20:09:22.029][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:22.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-11-27 20:09:22.036][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-11-27 20:09:22.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-11-27 20:09:22.042][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:22.044][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:22.045][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:22.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:22.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:22.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:22.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:22.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:22.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:22.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:22.070][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.074][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.081][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:22.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:22.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.086][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.087][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:22.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:22.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.091][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:22.094][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:22.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.096][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:22.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:22.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.105][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:22.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:22.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.110][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:22.112][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:22.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.115][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.117][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:22.119][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:22.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.124][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:22.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:22.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.128][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.130][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:22.132][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:22.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:22.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:22.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.142][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:22.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:22.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:22.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:22.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:22.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:22.200][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-27 20:09:22.202][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-27 20:09:22.222][biodb::testThat]
biodb.INFO [2024-11-27 20:09:22.224][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-27 20:09:22.226][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:22.228][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:22.251][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-27 20:09:22.252][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-27 20:09:22.254][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-27 20:09:22.256][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-27 20:09:22.258][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-11-27 20:09:22.260][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:22.261][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:22.262][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:22.264][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:22.265][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:22.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:22.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:22.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:22.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:22.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:22.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:22.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:22.289][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-11-27 20:09:22.293][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:22.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:22.296][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-11-27 20:09:22.645][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-11-27 20:09:23.001][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:23.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-11-27 20:09:23.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-11-27 20:09:23.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:23.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:23.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:28.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:28.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:28.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:28.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:28.453][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-11-27 20:09:28.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:28.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:28.461][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-11-27 20:09:28.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-11-27 20:09:29.238][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:29.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-11-27 20:09:29.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-11-27 20:09:29.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:29.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:29.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:29.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:29.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:29.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:29.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:29.724][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-11-27 20:09:29.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:29.729][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:29.731][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-11-27 20:09:30.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-11-27 20:09:30.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:30.431][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-11-27 20:09:30.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-11-27 20:09:30.436][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-11-27 20:09:30.439][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:30.440][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-27 20:09:30.441][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:30.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:30.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:30.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:30.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:30.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:30.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:30.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:30.453][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.454][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.455][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.460][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:30.461][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:30.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.462][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.463][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:30.464][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:30.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.466][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.467][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:30.468][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:30.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.469][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.470][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.471][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.473][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.474][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.475][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.477][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:30.478][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:30.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.480][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.482][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.483][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.484][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:30.485][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:30.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.488][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:30.489][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:30.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.490][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.491][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:30.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:30.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:30.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:30.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:30.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:30.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:30.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:30.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:30.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:30.531][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.532][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.533][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.554][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:30.555][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:30.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.556][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.557][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:30.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:30.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.561][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:30.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:30.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.563][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:30.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:30.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.567][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:30.568][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:30.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:30.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.574][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.575][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.577][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.581][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.582][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.583][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.588][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:30.589][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:30.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.590][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:30.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:30.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.597][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.602][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:30.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:30.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.604][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:30.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:30.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.608][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:30.609][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:30.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.612][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:30.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:30.616][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:30.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.618][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:30.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:30.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:30.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:30.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:30.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:30.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:30.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:30.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:30.656][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.TRACE[2024-11-27 20:09:30.658][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.660][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.665][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:30.666][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:30.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.668][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:30.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:30.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.672][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:30.673][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:30.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.675][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.676][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:30.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:30.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:30.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:30.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.682][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:30.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.686][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.688][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:30.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.693][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.694][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.695][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.696][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:30.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.700][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:30.700][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:30.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.703][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.706][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.709][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:30.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.713][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:30.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:30.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.716][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:30.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:30.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.720][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:30.721][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:30.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.723][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.724][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:30.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:30.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:30.728][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:30.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.730][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.731][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:30.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:30.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:30.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:30.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:30.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:30.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:30.788][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-27 20:09:30.789][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-27 20:09:30.789][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-27 20:09:30.806][biodb::testThat]
biodb.INFO [2024-11-27 20:09:30.807][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-27 20:09:30.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:30.808][biodb::testThat]
biodb.INFO [2024-11-27 20:09:30.832][biodb::testThat]
biodb.INFO [2024-11-27 20:09:30.833][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-27 20:09:30.833][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:30.834][biodb::testThat]
biodb.INFO [2024-11-27 20:09:30.846][biodb::testThat]
biodb.INFO [2024-11-27 20:09:30.847][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-27 20:09:30.848][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:30.848][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:30.850][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:30.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:30.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:30.856][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:31.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:31.848][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:31.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-11-27 20:09:31.861][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-11-27 20:09:31.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:31.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:31.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:31.875][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:31.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:31.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:31.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:31.878][ef$get] fields variable is a list.
biodb.INFO [2024-11-27 20:09:31.879][biodb::testThat]
biodb.INFO [2024-11-27 20:09:31.880][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-27 20:09:31.881][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:31.881][biodb::testThat]
biodb.ERROR[2024-11-27 20:09:31.893][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-27 20:09:31.907][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-27 20:09:31.919][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:09:31.920][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:09:31.921][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:09:31.922][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:09:31.923][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:31.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:31.924][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:31.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:31.926][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:09:31.935][biodb::testContext]
biodb.INFO [2024-11-27 20:09:31.936][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:31.937][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-27 20:09:31.938][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:31.939][biodb::testContext]
biodb.INFO [2024-11-27 20:09:31.941][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:31.942][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:31.945][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:31.946][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:09:31.947][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.950][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:09:31.951][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.954][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:09:31.955][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.957][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[2024-11-27 20:09:31.958][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:09:31.959][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:09:31.960][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:09:31.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.963][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:09:31.964][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:09:31.965][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.968][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:09:31.968][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:09:31.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.971][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:09:31.972][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:09:31.973][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:09:31.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.976][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:09:31.977][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.980][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:09:31.981][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:09:31.982][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:09:31.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.985][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:31.985][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:09:31.986][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:09:31.987][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:09:31.988][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:09:31.989][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:09:31.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.992][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:09:31.993][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:09:31.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:31.996][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:09:31.996][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:09:31.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:31.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:31.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.000][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:09:32.000][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:09:32.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.003][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:09:32.004][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:09:32.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.020][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:09:32.021][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:09:32.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.024][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[2024-11-27 20:09:32.024][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:32.025][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:09:32.338][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:09:32.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.341][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:09:32.342][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:09:32.343][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:09:32.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.346][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:09:32.348][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.349][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:09:32.350][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.351][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:32.351][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.352][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.353][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.355][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:32.356][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:32.357][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.358][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:09:32.359][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:32.360][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.361][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.363][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:32.363][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:32.363][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:32.363][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:32.363][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:32.364][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:32.365][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.367][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:32.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.370][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.371][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.372][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:32.373][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:32.374][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.374][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.375][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:09:32.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.378][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:32.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.379][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:32.380][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.381][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.382][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.383][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.384][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:32.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:32.385][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.386][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:09:32.387][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:32.388][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.389][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.390][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:32.390][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:32.390][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:32.390][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:32.390][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:32.391][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:32.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:32.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.398][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:32.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:32.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.402][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.403][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:09:32.404][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.405][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:09:32.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.408][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:32.409][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.411][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.414][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:32.415][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:32.416][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.416][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:09:32.417][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:32.418][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.419][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.421][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:32.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:32.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.429][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:32.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:32.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.433][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.435][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:09:32.437][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.438][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:32.439][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.440][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:32.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.442][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.443][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.444][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:32.445][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:32.446][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.448][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:09:32.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:32.450][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.453][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.454][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:32.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:32.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.462][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:32.464][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:32.465][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.466][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:32.468][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:32.469][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.530][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.DEBUG[2024-11-27 20:09:32.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.552][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:09:32.554][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:09:32.555][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:09:32.557][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:09:32.559][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:32.560][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:09:32.561][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:32.563][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:32.564][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:09:32.566][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:09:32.568][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:32.569][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:09:32.571][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:32.572][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:32.574][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:09:32.575][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:09:32.576][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:09:32.578][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:09:32.579][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:32.581][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:09:32.582][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:09:32.584][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:09:32.586][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:09:32.588][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:09:32.590][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:09:32.592][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:09:32.593][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:09:32.595][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:09:32.596][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:09:32.598][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:09:32.599][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:09:32.601][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:09:32.603][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:09:32.605][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:09:32.607][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:09:32.608][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:09:32.610][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:09:32.611][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:09:32.613][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:09:32.615][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:09:32.616][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:09:32.617][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:09:32.618][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:09:32.620][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:09:32.621][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:09:32.623][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:09:32.624][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:09:32.625][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:09:32.627][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:09:32.629][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:09:32.631][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:09:32.633][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:09:32.634][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:09:32.636][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:09:32.638][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:09:32.640][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:09:32.641][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:09:32.643][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:09:32.644][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:09:32.646][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:09:32.647][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:09:32.648][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:09:32.650][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:09:32.651][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:09:32.653][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:09:32.655][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:09:32.656][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:32.658][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:32.659][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:09:32.661][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:09:32.663][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:09:32.665][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:09:32.667][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:09:32.669][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:09:32.670][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:09:32.672][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:09:32.673][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:09:32.675][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:09:32.676][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:09:32.678][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:09:32.679][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:09:32.680][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:09:32.681][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:09:32.682][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:09:32.684][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:32.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:32.686][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.709][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[2024-11-27 20:09:32.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:32.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:32.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:32.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:32.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:32.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:32.816][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:32.842][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:09:32.844][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.845][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.846][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.848][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:32.849][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.850][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.851][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.852][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:09:32.852][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:09:32.853][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:32.854][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.855][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:09:32.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:09:32.857][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:09:32.858][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:32.859][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:32.859][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:32.859][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:32.860][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:09:32.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.863][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:32.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:32.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:32.866][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:32.867][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:32.867][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:09:32.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:32.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:32.872][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:32.873][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:09:32.873][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:09:32.881][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:32.883][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:32.885][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:09:32.887][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:32.889][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:32.892][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:32.896][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:09:32.897][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:09:32.898][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:09:32.900][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:09:32.902][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:32.903][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:32.905][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:09:32.907][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:09:32.909][biodb::testThat]
biodb.INFO [2024-11-27 20:09:32.910][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-27 20:09:32.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:32.913][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:32.927][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:09:32.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:32.955][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:32.956][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-11-27 20:09:33.289][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-11-27 20:09:33.782][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:33.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-11-27 20:09:33.789][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-11-27 20:09:33.796][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:33.801][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:33.802][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:33.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:34.149][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:34.492][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:34.495][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-11-27 20:09:34.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-11-27 20:09:34.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:34.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:34.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:34.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:34.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:34.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:34.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:34.511][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:34.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:34.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:34.519][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:34.864][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:35.214][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:35.216][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-11-27 20:09:35.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-11-27 20:09:35.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.292][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:35.296][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:35.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-27 20:09:35.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:35.303][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-27 20:09:35.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:35.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:35.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-27 20:09:35.335][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:35.338][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-27 20:09:35.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.383][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[2024-11-27 20:09:35.388][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:35.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-27 20:09:35.392][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:35.395][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-27 20:09:35.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:35.421][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:35.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-27 20:09:35.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:35.428][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-27 20:09:35.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:35.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:35.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:35.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:35.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:35.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:35.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:35.452][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:35.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:35.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:35.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:35.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:36.168][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:36.172][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-11-27 20:09:36.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-11-27 20:09:36.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:36.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:36.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:36.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:36.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:36.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:36.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:09:36.245][biodb::testThat]
biodb.INFO [2024-11-27 20:09:36.246][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-27 20:09:36.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:36.249][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:36.253][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:36.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:36.259][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:36.263][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:36.621][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:36.966][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:36.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-11-27 20:09:36.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-11-27 20:09:36.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:36.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:36.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:36.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:36.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:36.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:36.992][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.DEBUG[2024-11-27 20:09:36.997][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:37.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:37.004][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:37.006][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:37.353][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:37.697][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:37.701][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-11-27 20:09:37.708][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-11-27 20:09:37.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:37.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:37.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:37.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:37.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:37.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:09:37.751][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:09:37.753][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:09:37.755][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:09:37.757][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:09:37.758][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:37.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:37.761][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:37.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:37.764][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:09:37.770][biodb::testContext]
biodb.INFO [2024-11-27 20:09:37.771][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:37.773][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-27 20:09:37.774][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:37.775][biodb::testContext]
biodb.INFO [2024-11-27 20:09:37.779][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:37.781][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:37.788][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:37.789][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:09:37.790][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.794][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:09:37.796][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.800][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:09:37.829][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.834][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.DEBUG[2024-11-27 20:09:37.835][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:09:37.837][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:09:37.838][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:09:37.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.841][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:09:37.843][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:09:37.844][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.849][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:09:37.850][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:09:37.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.855][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:09:37.855][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:09:37.856][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:09:37.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.860][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:09:37.861][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.865][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:09:37.866][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:09:37.867][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:09:37.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.872][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:37.873][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:09:37.874][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:09:37.875][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:09:37.876][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:09:37.877][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:09:37.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.880][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:09:37.881][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:09:37.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.885][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:09:37.886][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:09:37.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.890][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:09:37.891][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:09:37.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.894][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:09:37.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:09:37.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.899][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:09:37.900][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:09:37.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:37.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:37.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:37.903][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:37.904][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:09:38.011][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:09:38.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.026][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:09:38.027][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:09:38.028][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:09:38.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.032][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:09:38.034][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.036][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:09:38.038][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.039][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:38.040][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.041][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.042][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.043][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.044][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:38.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:38.047][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.048][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:09:38.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:38.050][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:38.052][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:38.053][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:38.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.056][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:38.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.059][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.060][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:38.061][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:38.062][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.063][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.065][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:09:38.068][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.071][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:38.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.074][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:38.076][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.077][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.078][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.078][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.080][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:38.081][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:38.082][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.083][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:09:38.084][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:38.085][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.086][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.088][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:38.088][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:38.088][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:38.088][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:38.088][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:38.089][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:38.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:38.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.095][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.097][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:38.098][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:38.099][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.100][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.101][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:09:38.103][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.105][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:09:38.106][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.107][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:38.108][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.109][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.112][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:38.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:38.115][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.117][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:09:38.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:38.118][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.120][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.121][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:38.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:38.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.130][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:38.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:38.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.134][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.135][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:09:38.137][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.137][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:38.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:38.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.143][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.144][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:38.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:38.146][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.147][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:09:38.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:38.150][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.151][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.152][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.153][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:38.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.156][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:38.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.159][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.160][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:38.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:38.162][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.163][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:38.165][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:38.166][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.241][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:09:38.243][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:09:38.244][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:09:38.246][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:09:38.247][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:38.248][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:09:38.250][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:38.252][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:38.253][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:09:38.255][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:09:38.257][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:38.259][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:09:38.262][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:38.263][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:38.265][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:09:38.266][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:09:38.268][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:09:38.269][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:09:38.270][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:38.271][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:09:38.272][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:09:38.273][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:09:38.275][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:09:38.276][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:09:38.277][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:09:38.278][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:09:38.279][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:09:38.281][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:09:38.282][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:09:38.283][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:09:38.284][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:09:38.286][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:09:38.287][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:09:38.288][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:09:38.289][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:09:38.290][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:09:38.291][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:09:38.294][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:09:38.296][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:09:38.298][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:09:38.300][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:09:38.308][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:09:38.309][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:09:38.310][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:09:38.311][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:09:38.312][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:09:38.314][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:09:38.315][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:09:38.316][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:09:38.317][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:09:38.318][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:09:38.320][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:09:38.322][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:09:38.323][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:09:38.324][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:09:38.325][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:09:38.326][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:09:38.328][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:09:38.329][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:09:38.330][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:09:38.331][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:09:38.333][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:09:38.334][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:09:38.336][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:09:38.338][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:09:38.340][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:09:38.341][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:38.343][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:38.344][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:09:38.346][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:09:38.347][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:09:38.349][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:09:38.350][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:09:38.352][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:09:38.353][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:09:38.354][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:09:38.356][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:09:38.358][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:09:38.359][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:09:38.361][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:09:38.364][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:09:38.365][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:09:38.366][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:09:38.368][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:09:38.370][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:38.371][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:38.372][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.373][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:38.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:38.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:38.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:38.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:38.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:38.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:38.487][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:38.490][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:09:38.492][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.493][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:38.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.498][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.500][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:09:38.500][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:09:38.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:38.502][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.503][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:09:38.504][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:09:38.505][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:09:38.506][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:38.506][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:38.506][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:38.506][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:38.507][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:09:38.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:38.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:38.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:38.513][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:38.514][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:38.514][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:09:38.515][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:38.516][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:38.517][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:38.518][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:09:38.518][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:09:38.523][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:38.524][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:38.525][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:09:38.526][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:38.528][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:38.529][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:38.531][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:09:38.532][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:09:38.533][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:09:38.535][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:09:38.537][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:38.538][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:38.540][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:09:38.540][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:09:38.542][biodb::testThat]
biodb.INFO [2024-11-27 20:09:38.543][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-27 20:09:38.544][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:38.545][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:38.548][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:09:38.565][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:38.567][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:09:38.568][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:38.569][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:09:38.573][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:38.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:38.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:38.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-27 20:09:38.929][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-27 20:09:39.277][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:39.280][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-11-27 20:09:39.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-11-27 20:09:39.299][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:09:39.301][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:09:39.303][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:09:39.304][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:09:39.305][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.306][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.308][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-27 20:09:39.316][biodb::testContext]
biodb.INFO [2024-11-27 20:09:39.317][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:39.318][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-27 20:09:39.319][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-27 20:09:39.321][biodb::testContext]
biodb.INFO [2024-11-27 20:09:39.323][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:39.324][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:39.336][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:39.337][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-27 20:09:39.338][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.342][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-27 20:09:39.344][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.348][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-27 20:09:39.349][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.354][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-27 20:09:39.356][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-27 20:09:39.357][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-27 20:09:39.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.361][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-27 20:09:39.363][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-27 20:09:39.364][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.379][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-27 20:09:39.380][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-27 20:09:39.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.383][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-27 20:09:39.384][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-27 20:09:39.385][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-27 20:09:39.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.388][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-27 20:09:39.390][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.394][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.DEBUG[2024-11-27 20:09:39.396][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-27 20:09:39.397][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-27 20:09:39.399][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-27 20:09:39.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.403][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:39.403][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-27 20:09:39.405][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-27 20:09:39.406][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-27 20:09:39.407][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-27 20:09:39.408][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-27 20:09:39.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.414][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-27 20:09:39.416][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-27 20:09:39.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.419][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-27 20:09:39.420][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-27 20:09:39.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.424][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-27 20:09:39.424][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-27 20:09:39.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.429][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-27 20:09:39.430][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-27 20:09:39.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.434][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-27 20:09:39.436][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-27 20:09:39.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.441][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-27 20:09:39.442][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-27 20:09:39.527][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-27 20:09:39.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.533][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-27 20:09:39.534][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-27 20:09:39.536][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-27 20:09:39.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.541][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-27 20:09:39.543][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.544][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-27 20:09:39.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:39.547][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.548][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.549][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.550][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.551][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:39.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:39.552][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.553][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-27 20:09:39.554][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:39.555][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.556][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.557][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:39.557][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:39.557][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:39.557][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:39.557][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:39.558][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:39.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:39.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.565][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.566][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:39.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:39.570][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.571][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.572][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-27 20:09:39.575][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.576][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:39.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:39.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.584][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:39.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:39.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.586][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-27 20:09:39.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:39.588][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.589][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.590][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:39.590][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:39.590][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:39.590][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-27 20:09:39.590][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-27 20:09:39.591][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:39.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:39.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.598][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:39.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:39.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.602][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.604][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-27 20:09:39.605][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.606][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-27 20:09:39.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.608][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:39.608][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.609][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.610][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.612][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.612][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-27 20:09:39.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:39.615][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.616][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-27 20:09:39.618][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:39.619][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.621][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:39.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:39.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.627][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.628][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:39.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:39.630][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.631][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.632][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-27 20:09:39.634][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.635][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-27 20:09:39.635][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:39.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.642][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-27 20:09:39.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:39.644][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.645][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-27 20:09:39.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:39.648][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.648][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:39.650][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-27 20:09:39.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.652][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.653][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:39.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:39.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:39.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:39.656][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.657][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:39.658][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:39.659][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:39.660][self$setPropertyValue]
biodb.DEBUG[2024-11-27 20:09:39.661][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:39.662][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.706][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[2024-11-27 20:09:39.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.717][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[2024-11-27 20:09:39.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.725][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[2024-11-27 20:09:39.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.732][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[2024-11-27 20:09:39.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.737][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[2024-11-27 20:09:39.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.757][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-27 20:09:39.758][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-27 20:09:39.759][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-27 20:09:39.761][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-27 20:09:39.762][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:39.763][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-27 20:09:39.764][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:39.766][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:39.767][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-27 20:09:39.769][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-27 20:09:39.770][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:39.772][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-27 20:09:39.773][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-27 20:09:39.774][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-27 20:09:39.775][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-27 20:09:39.776][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-27 20:09:39.778][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-27 20:09:39.779][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-27 20:09:39.780][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:39.781][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-27 20:09:39.783][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-27 20:09:39.785][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-27 20:09:39.787][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-27 20:09:39.788][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-27 20:09:39.790][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-27 20:09:39.792][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-27 20:09:39.793][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-27 20:09:39.795][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-27 20:09:39.796][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-27 20:09:39.797][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-27 20:09:39.798][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-27 20:09:39.800][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-27 20:09:39.801][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-27 20:09:39.802][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-27 20:09:39.803][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-27 20:09:39.804][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-27 20:09:39.806][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-27 20:09:39.808][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-27 20:09:39.809][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-27 20:09:39.810][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-27 20:09:39.811][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-27 20:09:39.813][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-27 20:09:39.815][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-27 20:09:39.817][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-27 20:09:39.819][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-27 20:09:39.820][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-27 20:09:39.822][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-27 20:09:39.823][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-27 20:09:39.830][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-27 20:09:39.832][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-27 20:09:39.835][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-27 20:09:39.837][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-27 20:09:39.838][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-27 20:09:39.839][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-27 20:09:39.840][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-27 20:09:39.841][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-27 20:09:39.843][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-27 20:09:39.845][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-27 20:09:39.847][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-27 20:09:39.849][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-27 20:09:39.850][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-27 20:09:39.851][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-27 20:09:39.852][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-27 20:09:39.853][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-27 20:09:39.855][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-27 20:09:39.856][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-27 20:09:39.857][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:39.859][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:39.861][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-27 20:09:39.863][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-27 20:09:39.864][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-27 20:09:39.865][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-27 20:09:39.866][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-27 20:09:39.869][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-27 20:09:39.871][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-27 20:09:39.873][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-27 20:09:39.874][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-27 20:09:39.875][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-27 20:09:39.878][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-27 20:09:39.895][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-27 20:09:39.896][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-27 20:09:39.898][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-27 20:09:39.899][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-27 20:09:39.900][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-27 20:09:39.902][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2024-11-27 20:09:39.903][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-27 20:09:39.904][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.907][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.966][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.DEBUG[2024-11-27 20:09:39.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:39.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:39.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:39.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:39.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:39.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:39.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:39.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.003][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[2024-11-27 20:09:40.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:40.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.010][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[2024-11-27 20:09:40.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:40.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:40.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:40.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.024][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[2024-11-27 20:09:40.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:40.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:40.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-27 20:09:40.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:40.038][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-27 20:09:40.062][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-27 20:09:40.066][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:40.067][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-27 20:09:40.068][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:40.069][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-27 20:09:40.070][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:40.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-27 20:09:40.072][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:40.072][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-27 20:09:40.073][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-27 20:09:40.074][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-27 20:09:40.075][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:40.076][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-27 20:09:40.077][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-27 20:09:40.078][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-27 20:09:40.079][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-27 20:09:40.079][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-27 20:09:40.079][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-27 20:09:40.079][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-27 20:09:40.081][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-27 20:09:40.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:40.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:40.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-27 20:09:40.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-27 20:09:40.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-27 20:09:40.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-27 20:09:40.090][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:40.090][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-27 20:09:40.090][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-27 20:09:40.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-27 20:09:40.092][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-27 20:09:40.093][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-27 20:09:40.093][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-27 20:09:40.100][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-27 20:09:40.102][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-27 20:09:40.104][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-27 20:09:40.105][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-27 20:09:40.106][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-27 20:09:40.108][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-27 20:09:40.112][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-27 20:09:40.113][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-27 20:09:40.114][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-27 20:09:40.116][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-27 20:09:40.117][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:40.118][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-27 20:09:40.119][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-27 20:09:40.120][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-27 20:09:40.122][biodb::testThat]
biodb.INFO [2024-11-27 20:09:40.122][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-27 20:09:40.123][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-27 20:09:40.124][biodb::testThat]
biodb.DEBUG[2024-11-27 20:09:40.127][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-27 20:09:40.146][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:40.147][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-27 20:09:40.148][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:40.150][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-27 20:09:40.153][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-27 20:09:40.156][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-27 20:09:40.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-27 20:09:40.159][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-27 20:09:40.161][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-27 20:09:40.166][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-27 20:09:40.168][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-27 20:09:40.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-27 20:09:40.171][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-27 20:09:40.172][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-27 20:09:40.173][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-27 20:09:40.175][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-27 20:09:40.176][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-27 20:09:40.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-27 20:09:40.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:40.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:40.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:40.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:40.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:40.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:40.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-27 20:09:40.194][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-11-27 20:09:40.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-27 20:09:40.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-27 20:09:40.198][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-11-27 20:09:40.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-11-27 20:09:41.651][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-27 20:09:41.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-11-27 20:09:41.661][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-11-27 20:09:41.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-11-27 20:09:41.667][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-27 20:09:41.668][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-27 20:09:41.669][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-27 20:09:41.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-27 20:09:41.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:41.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:41.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:41.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:41.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:41.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-27 20:09:41.688][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.692][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.697][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:41.698][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:41.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.700][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-27 20:09:41.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-27 20:09:41.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.720][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:41.721][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:41.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.724][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-27 20:09:41.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-27 20:09:41.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.733][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-27 20:09:41.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-27 20:09:41.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.736][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.738][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-27 20:09:41.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-27 20:09:41.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.742][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:41.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:41.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.748][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:41.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-27 20:09:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.758][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:41.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:41.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.760][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.762][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-27 20:09:41.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-27 20:09:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:41.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:41.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.770][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:41.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-27 20:09:41.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.776][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:41.779][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:41.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.781][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-27 20:09:41.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-27 20:09:41.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.786][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:41.787][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:41.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.789][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.790][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-27 20:09:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-27 20:09:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:41.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:41.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.798][ef$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-27 20:09:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-27 20:09:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-27 20:09:41.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-27 20:09:41.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-27 20:09:41.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-27 20:09:41.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-27 20:09:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-27 20:09:41.852][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-27 20:09:41.859][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-27 20:09:41.861][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-27 20:09:41.861][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-27 20:09:41.862][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-27 20:09:41.863][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-27 20:09:41.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-27 20:09:41.865][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-27 20:09:41.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-27 20:09:41.866][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-27 20:09:41.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
17.545 2.035 73.370
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.742 | 1.850 | 56.404 | |
| ChebiEntry | 0.318 | 0.021 | 0.360 | |