Pierrick Roger
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-11-19 19:55:14 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 20:01:35 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 381.4 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.12.0’
* 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 2.845 1.93 16.244
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 [2024-11-19 20:00:54.919][biodb::testContext]
biodb.INFO [2024-11-19 20:00:54.924][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:00:54.926][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-19 20:00:54.927][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:00:54.928][biodb::testContext]
biodb.INFO [2024-11-19 20:00:54.937][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:00:54.939][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 20:00:54.956][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:00:54.957][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 20:00:54.958][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 20:00:54.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:54.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:54.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:54.963][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 20:00:55.011][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 20:00:55.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.025][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[2024-11-19 20:00:55.027][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 20:00:55.029][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 20:00:55.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.075][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 20:00:55.077][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 20:00:55.104][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 20:00:55.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.112][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 20:00:55.113][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 20:00:55.115][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 20:00:55.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.119][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 20:00:55.121][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 20:00:55.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.125][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 20:00:55.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 20:00:55.127][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 20:00:55.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.130][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 20:00:55.131][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 20:00:55.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.135][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 20:00:55.135][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 20:00:55.137][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 20:00:55.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.141][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:00:55.143][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 20:00:55.144][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 20:00:55.146][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 20:00:55.147][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 20:00:55.148][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 20:00:55.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.151][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.DEBUG[2024-11-19 20:00:55.152][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 20:00:55.153][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 20:00:55.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.157][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 20:00:55.158][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 20:00:55.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.161][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 20:00:55.162][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 20:00:55.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.166][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 20:00:55.167][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 20:00:55.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.171][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 20:00:55.172][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 20:00:55.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.178][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:00:55.179][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 20:00:55.272][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-19 20:00:55.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.278][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 20:00:55.280][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 20:00:55.281][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 20:00:55.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.290][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 20:00:55.332][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.355][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 20:00:55.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.359][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:00:55.360][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.364][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.368][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:00:55.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:00:55.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.374][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 20:00:55.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:00:55.377][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.378][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.379][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:00:55.379][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:00:55.379][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:00:55.379][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:00:55.379][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:00:55.381][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:00:55.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.384][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:00:55.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.388][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.390][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.391][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:00:55.392][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:00:55.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.395][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.397][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 20:00:55.399][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.401][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:00:55.402][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:00:55.404][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.410][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:00:55.411][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:00:55.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.414][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 20:00:55.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:00:55.417][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:00:55.419][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:00:55.419][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:00:55.419][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:00:55.419][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:00:55.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:00:55.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.423][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:00:55.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.427][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.429][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:00:55.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:00:55.432][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.433][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.435][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 20:00:55.437][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.439][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 20:00:55.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:00:55.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:00:55.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:00:55.458][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.460][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 20:00:55.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:00:55.462][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.465][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:00:55.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.471][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:00:55.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.474][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.475][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.476][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:00:55.477][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:00:55.479][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.480][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.482][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 20:00:55.484][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.486][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:00:55.487][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.489][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:00:55.490][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.492][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.494][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.495][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:00:55.496][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:00:55.497][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.498][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 20:00:55.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:00:55.500][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.501][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.503][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:00:55.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:00:55.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.512][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:00:55.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:00:55.515][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.516][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:00:55.521][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:00:55.522][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.535][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[2024-11-19 20:00:55.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.547][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[2024-11-19 20:00:55.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.574][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[2024-11-19 20:00:55.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.579][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[2024-11-19 20:00:55.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.620][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 20:00:55.627][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 20:00:55.629][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 20:00:55.632][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 20:00:55.634][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:00:55.636][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 20:00:55.638][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 20:00:55.640][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 20:00:55.642][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 20:00:55.644][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 20:00:55.645][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:00:55.647][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 20:00:55.649][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 20:00:55.650][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 20:00:55.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 20:00:55.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 20:00:55.655][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 20:00:55.656][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 20:00:55.658][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:00:55.660][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 20:00:55.662][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 20:00:55.663][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 20:00:55.665][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 20:00:55.666][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 20:00:55.668][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 20:00:55.670][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 20:00:55.672][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 20:00:55.673][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 20:00:55.675][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 20:00:55.676][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 20:00:55.678][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 20:00:55.680][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 20:00:55.682][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 20:00:55.683][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 20:00:55.684][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 20:00:55.686][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 20:00:55.688][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 20:00:55.690][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 20:00:55.691][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 20:00:55.693][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 20:00:55.695][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 20:00:55.697][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 20:00:55.699][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 20:00:55.706][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 20:00:55.708][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 20:00:55.710][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 20:00:55.712][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 20:00:55.713][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 20:00:55.714][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 20:00:55.716][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 20:00:55.717][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 20:00:55.719][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 20:00:55.721][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 20:00:55.722][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 20:00:55.724][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 20:00:55.726][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 20:00:55.727][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 20:00:55.728][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 20:00:55.730][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 20:00:55.731][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 20:00:55.733][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 20:00:55.734][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 20:00:55.736][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 20:00:55.737][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 20:00:55.739][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 20:00:55.740][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 20:00:55.744][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:00:55.746][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:00:55.747][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 20:00:55.749][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 20:00:55.751][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 20:00:55.752][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 20:00:55.754][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 20:00:55.755][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 20:00:55.757][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 20:00:55.759][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 20:00:55.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 20:00:55.762][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 20:00:55.764][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 20:00:55.765][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 20:00:55.767][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 20:00:55.769][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 20:00:55.771][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 20:00:55.779][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 20:00:55.781][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:00:55.785][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:00:55.786][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.789][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.853][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[2024-11-19 20:00:55.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.871][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[2024-11-19 20:00:55.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.885][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[2024-11-19 20:00:55.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.901][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[2024-11-19 20:00:55.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:00:55.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:55.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:55.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:55.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:55.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:55.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:00:55.937][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 20:00:55.957][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 20:00:55.960][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.961][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.963][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:00:55.965][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.968][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.969][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 20:00:55.971][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 20:00:55.972][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:00:55.973][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.975][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 20:00:55.976][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 20:00:55.977][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 20:00:55.979][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 20:00:55.980][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:00:55.980][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:00:55.980][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:00:55.982][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 20:00:55.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:00:55.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:00:55.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:00:55.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:00:55.991][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:00:55.991][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 20:00:55.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:00:55.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:00:55.994][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 20:00:55.996][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 20:00:55.996][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 20:00:56.005][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:00:56.007][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:00:56.009][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 20:00:56.011][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:00:56.014][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:00:56.016][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:00:56.053][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 20:00:56.054][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 20:00:56.060][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 20:00:56.066][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 20:00:56.072][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:00:56.074][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:00:56.076][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 20:00:56.077][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 20:00:56.091][biodb::testThat]
biodb.INFO [2024-11-19 20:00:56.093][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-19 20:00:56.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:56.095][biodb::testThat]
biodb.TRACE[2024-11-19 20:00:56.104][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-19 20:00:56.106][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:00:56.110][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:00:56.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:00:56.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:56.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:56.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:56.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:56.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:56.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:00:56.163][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.164][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.166][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.186][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.187][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.189][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.219][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.221][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.222][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.238][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:56.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:56.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.241][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.248][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.253][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.254][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.256][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.258][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.261][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:00:56.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.264][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.265][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:00:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.268][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.269][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.272][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.278][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.281][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.289][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:00:56.290][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.292][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:00:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.298][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.299][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.301][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:00:56.389][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-19 20:00:56.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:56.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:56.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:56.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:56.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.490][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:56.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:56.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:56.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:56.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:56.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:56.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.631][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.632][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.634][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:56.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:56.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.668][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.670][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.671][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.699][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.700][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.701][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:56.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:56.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.716][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.731][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.732][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.734][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.762][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.816][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.817][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.820][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:56.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.837][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.848][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.861][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.862][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.866][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:56.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:56.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.884][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.891][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.902][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.905][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.906][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:56.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.928][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.933][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.938][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.939][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.941][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:56.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.974][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.978][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.979][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:56.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:56.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.994][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:56.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.008][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.009][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.012][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.044][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.063][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.067][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.081][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:57.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:57.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.084][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.090][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:57.092][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:57.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.094][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.100][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.101][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.112][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.120][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.122][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.128][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.131][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.139][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.141][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.151][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 20:00:57.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:57.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.156][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.162][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.166][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:57.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:57.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.176][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 20:00:57.191][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.192][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-19 20:00:57.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.194][biodb::testThat]
biodb.DEBUG[2024-11-19 20:00:57.212][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-19 20:00:57.220][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:00:57.225][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-19 20:00:57.227][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:00:57.231][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-19 20:00:57.233][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:00:57.262][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:00:57.264][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:00:57.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:00:57.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:00:57.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:00:57.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:00:57.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:00:57.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:00:57.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:00:57.280][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.281][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.318][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:57.319][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:57.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.322][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:00:57.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:00:57.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.328][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:57.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:57.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.331][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:00:57.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:00:57.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.339][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.341][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.351][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.357][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.359][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.361][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:00:57.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.366][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:00:57.367][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.369][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.371][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:00:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.378][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.387][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.391][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.398][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:00:57.399][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:57.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.400][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.402][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:00:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:00:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.407][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:57.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:57.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.411][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:00:57.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:00:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:00:57.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:00:57.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:00:57.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:00:57.465][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-19 20:00:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-19 20:00:57.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-19 20:00:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-19 20:00:57.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-19 20:00:57.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-19 20:00:57.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-19 20:00:57.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:00:57.498][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.499][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-19 20:00:57.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.502][biodb::testThat]
biodb.TRACE[2024-11-19 20:00:57.505][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.508][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:00:57.510][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-19 20:00:57.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:00:57.562][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-19 20:00:57.568][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 20:00:57.591][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:00:57.613][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 20:00:57.615][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:00:57.618][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 20:00:57.643][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[2024-11-19 20:00:57.652][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:00:57.660][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:00:57.662][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:00:57.664][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:00:57.666][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-19 20:00:57.682][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.683][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:00:57.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.686][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.687][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.688][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.691][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 20:00:57.696][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.698][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-19 20:00:57.699][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.699][biodb::testThat]
biodb.TRACE[2024-11-19 20:00:57.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:00:57.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:00:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:00:57.795][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[2024-11-19 20:00:57.799][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:00:57.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:00:57.802][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:00:57.804][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-19 20:00:57.833][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.834][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-19 20:00:57.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.836][biodb::testThat]
biodb.TRACE[2024-11-19 20:00:57.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.884][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.890][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:57.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:57.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.900][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:57.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:57.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:00:57.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:00:57.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:00:57.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:00:57.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 20:00:57.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:57.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 20:00:57.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:00:57.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:57.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 20:00:57.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:00:57.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:00:57.975][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.976][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-19 20:00:57.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.978][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.989][biodb::testThat]
biodb.INFO [2024-11-19 20:00:57.991][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-19 20:00:57.992][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:57.993][biodb::testThat]
biodb.INFO [2024-11-19 20:00:58.009][biodb::testThat]
biodb.INFO [2024-11-19 20:00:58.010][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-19 20:00:58.011][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:58.012][biodb::testThat]
biodb.DEBUG[2024-11-19 20:00:58.016][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-19 20:00:58.635][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-19 20:00:59.736][biodb::testThat]
biodb.INFO [2024-11-19 20:00:59.737][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-19 20:00:59.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:00:59.740][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:00.360][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[2024-11-19 20:01:00.755][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:00.757][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:00.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:00.759][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:00.760][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:00.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:00.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:00.762][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:00.764][biodb::testThat]
biodb.INFO [2024-11-19 20:01:00.765][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-19 20:01:00.766][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:00.767][biodb::testThat]
biodb.TRACE[2024-11-19 20:01:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:00.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:00.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:00.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:00.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:00.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:00.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:00.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:00.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:00.985][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[2024-11-19 20:01:00.989][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:00.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:00.992][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:00.994][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:01:01.071][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[2024-11-19 20:01:01.073][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:01.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:01.076][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:01.078][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-11-19 20:01:01.098][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 20:01:01.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 20:01:01.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:01.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:01.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:01.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:01.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:01.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:01.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:01.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:01.144][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[2024-11-19 20:01:01.169][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:01.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 20:01:01.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:01.179][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 20:01:01.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:01.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:01.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:01.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:01.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:01.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:01.192][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[2024-11-19 20:01:01.193][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-19 20:01:01.233][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:01.235][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-19 20:01:01.236][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:01.237][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:01.238][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:01.239][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:01.240][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:01.241][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:01.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:01.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:01.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:01.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:01.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:01.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:01.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:01.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-19 20:01:01.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:01.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:01.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-19 20:01:01.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-19 20:01:01.964][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:01.992][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-19 20:01:02.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-19 20:01:02.008][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-19 20:01:02.011][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:02.013][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:02.014][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:02.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:02.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:02.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:02.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:02.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:02.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:02.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:02.033][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.034][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.036][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.051][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:02.053][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:02.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.055][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.056][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:02.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:02.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.061][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:02.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:02.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.065][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:02.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:02.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:02.073][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:02.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.074][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:02.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:02.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:02.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.082][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:02.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:02.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.087][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:02.088][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:02.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.091][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.092][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:02.093][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.095][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:02.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:02.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:02.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:02.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:02.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.113][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:02.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:02.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:02.119][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:02.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.121][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.130][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:02.131][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:02.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.133][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.134][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:02.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:02.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:02.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:02.178][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-19 20:01:02.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:02.201][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[2024-11-19 20:01:02.204][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:02.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 20:01:02.207][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:02.226][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 20:01:02.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:02.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:02.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:02.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:02.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:02.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:02.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:02.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:02.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:02.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:02.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:02.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:02.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:02.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:02.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:02.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:02.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:02.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:02.282][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-19 20:01:02.283][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:02.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-19 20:01:02.286][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:02.287][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:02.288][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:02.290][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:02.291][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:02.292][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:02.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:02.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:02.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:02.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:02.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:02.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:02.320][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[2024-11-19 20:01:02.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-19 20:01:02.334][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:02.335][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:02.349][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-19 20:01:02.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-19 20:01:03.060][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:03.062][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-19 20:01:03.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-19 20:01:03.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-19 20:01:03.084][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:03.086][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:03.087][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:03.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:03.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:03.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:03.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:03.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:03.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:03.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:03.105][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.106][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.108][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.113][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:03.114][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:03.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.116][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.118][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:03.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:03.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.122][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:03.124][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:03.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.126][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:03.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.132][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:03.133][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:03.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:03.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.142][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:03.143][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:03.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.145][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.151][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:03.153][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:03.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.155][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.156][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:03.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.159][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:03.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.165][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:03.166][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:03.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.169][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:03.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:03.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.174][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:03.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:03.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.178][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:03.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:03.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.183][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:03.184][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:03.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.186][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:03.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:03.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.191][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:03.192][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:03.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.193][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.194][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:03.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:03.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:03.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:03.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:03.243][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-19 20:01:03.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:03.288][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[2024-11-19 20:01:03.294][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:03.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:03.296][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:03.298][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:01:03.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:03.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:03.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:03.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:03.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:03.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:03.347][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.TRACE[2024-11-19 20:01:03.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:03.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:03.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:03.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:03.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:03.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:03.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:03.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:03.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:03.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:03.382][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[2024-11-19 20:01:03.383][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-19 20:01:03.390][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:03.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-19 20:01:03.393][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:03.395][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:03.396][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:03.397][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:03.398][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:03.399][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:03.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:03.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:03.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:03.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:03.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:03.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:03.413][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[2024-11-19 20:01:03.415][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-19 20:01:03.417][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:03.418][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:03.419][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-19 20:01:03.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-19 20:01:04.416][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:04.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-19 20:01:04.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-19 20:01:04.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-19 20:01:04.426][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:04.427][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:04.428][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:04.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:04.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:04.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:04.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:04.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:04.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:04.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:04.442][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.443][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.445][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.449][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:04.450][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:04.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.452][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.453][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:04.454][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:04.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.456][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.457][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:04.458][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:04.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.460][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:04.462][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:04.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.464][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.465][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:04.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:04.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.468][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.469][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:04.470][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.472][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.473][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:04.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:04.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.477][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:04.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:04.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.479][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:04.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:04.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.484][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:04.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:04.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.487][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.488][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:04.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:04.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.493][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:04.494][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:04.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:04.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:04.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:04.543][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-19 20:01:04.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:04.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:04.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:04.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:04.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:04.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:04.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:04.579][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[2024-11-19 20:01:04.580][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-19 20:01:04.580][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:04.582][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-19 20:01:04.583][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:04.584][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:04.585][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:04.586][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:04.587][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:04.587][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:04.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:04.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:04.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:04.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:04.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:04.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:04.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:04.599][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-19 20:01:04.603][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:04.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:04.605][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-19 20:01:04.939][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-19 20:01:05.271][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:05.274][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-19 20:01:05.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-19 20:01:05.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-19 20:01:05.292][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:05.294][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:05.295][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:05.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:05.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:05.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:05.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:05.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:05.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:05.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:05.314][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.315][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.320][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.327][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:05.329][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:05.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.331][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.333][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:05.334][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:05.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.339][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:05.340][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:05.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.343][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:05.346][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:05.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.351][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:05.352][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:05.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.355][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.357][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:05.357][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.360][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.362][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:05.363][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:05.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.366][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.368][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:05.369][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:05.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:05.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:05.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.380][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:05.382][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:05.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.384][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.386][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:05.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:05.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.392][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:05.393][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:05.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.396][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:05.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:05.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:05.454][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-19 20:01:05.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:05.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:05.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:05.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:05.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:05.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:05.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:05.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:05.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:05.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:05.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:05.497][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-19 20:01:05.498][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:05.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-19 20:01:05.502][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:05.503][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:05.504][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:05.505][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:05.506][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:05.507][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:05.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:05.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:05.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:05.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:05.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:05.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:05.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:05.525][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-19 20:01:05.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:05.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:05.531][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-19 20:01:05.863][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-19 20:01:06.207][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:06.209][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-19 20:01:06.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-19 20:01:06.217][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-19 20:01:06.219][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:06.221][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:06.222][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:06.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:06.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:06.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:06.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:06.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:06.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:06.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:06.241][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.245][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.250][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:06.251][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:06.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.253][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.254][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:06.256][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:06.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.258][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.260][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:06.291][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:06.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.293][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.294][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:06.295][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:06.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.297][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.299][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:06.300][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:06.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.302][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.303][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:06.305][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.307][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:06.310][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:06.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.314][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:06.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:06.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.317][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:06.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:06.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.323][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:06.324][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:06.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.326][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:06.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:06.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.333][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:06.334][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:06.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.336][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:06.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:06.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:06.388][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-19 20:01:06.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:06.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:06.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:06.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:06.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:06.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:06.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:06.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:06.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:06.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:06.434][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[2024-11-19 20:01:06.436][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-19 20:01:06.437][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:06.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-19 20:01:06.441][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:06.442][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:06.443][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:06.444][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:06.445][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:06.446][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:06.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:06.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:06.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:06.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:06.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:06.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:06.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:06.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-19 20:01:06.464][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:06.466][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:06.467][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-19 20:01:06.808][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-19 20:01:07.141][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:07.143][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-19 20:01:07.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-19 20:01:07.150][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-19 20:01:07.152][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:07.153][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:07.154][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:07.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:07.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:07.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:07.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:07.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:07.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:07.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:07.167][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.168][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.170][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.174][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:07.175][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:07.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.177][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:07.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.182][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:07.183][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:07.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.185][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.186][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.190][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:07.191][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:07.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.192][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:07.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:07.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.197][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:07.198][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:07.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.200][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:07.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:07.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.205][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:07.206][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:07.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.208][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:07.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.213][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:07.214][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.217][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:07.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:07.230][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:07.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.232][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:07.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.236][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:07.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:07.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.239][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:07.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.244][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:07.245][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:07.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.247][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:07.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:07.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.252][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:07.253][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:07.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.254][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.256][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:07.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:07.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:07.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:07.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:07.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:07.301][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-19 20:01:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:07.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:07.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:07.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:07.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:07.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:07.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:07.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:07.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:07.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:07.325][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-19 20:01:07.326][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:07.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-19 20:01:07.329][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:07.330][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:07.331][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:07.332][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:07.333][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:07.334][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:07.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:07.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:07.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:07.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:07.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:07.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:07.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:07.377][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-19 20:01:07.380][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:07.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:07.382][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-19 20:01:07.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-19 20:01:08.051][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:08.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-19 20:01:08.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-19 20:01:08.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-19 20:01:08.072][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:08.073][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:08.075][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:08.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:08.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:08.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:08.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:08.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:08.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:08.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:08.110][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.111][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.113][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.118][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:08.119][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:08.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.120][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:08.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:08.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.125][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:08.126][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:08.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.127][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:08.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:08.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.142][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:08.143][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:08.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.145][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:08.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.150][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:08.151][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:08.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.163][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.168][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:08.169][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:08.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.170][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.171][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:08.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:08.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.175][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:08.176][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.178][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.179][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:08.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:08.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:08.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.185][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:08.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.190][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:08.191][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:08.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.202][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:08.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:08.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.208][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:08.209][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:08.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.213][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:08.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.217][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:08.218][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:08.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.219][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:08.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:08.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:08.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:08.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:08.264][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-19 20:01:08.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:08.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:08.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:08.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:08.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:08.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:08.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:08.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:08.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:08.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:08.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:08.289][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-19 20:01:08.289][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:08.291][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-19 20:01:08.292][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:08.293][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:08.294][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:08.296][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:08.297][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:08.297][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:08.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:08.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:08.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:08.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:08.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:08.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:08.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:08.313][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-19 20:01:08.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:08.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:08.323][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-19 20:01:08.656][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-19 20:01:09.009][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:09.022][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-19 20:01:09.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-19 20:01:09.029][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-19 20:01:09.031][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:09.032][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:09.033][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:09.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:09.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:09.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:09.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:09.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:09.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:09.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:09.046][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.047][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.054][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:09.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:09.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.057][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.058][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:09.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:09.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.061][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:09.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:09.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.064][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:09.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:09.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:09.091][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:09.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:09.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:09.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.097][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:09.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:09.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.101][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:09.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:09.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.106][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:09.107][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:09.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.122][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:09.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.125][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:09.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.134][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:09.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:09.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.139][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:09.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.144][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:09.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:09.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.146][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:09.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.161][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:09.162][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:09.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.175][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.177][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:09.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:09.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.182][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:09.190][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:09.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.192][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:09.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:09.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:09.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:09.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:09.234][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-19 20:01:09.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:09.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:09.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:09.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:09.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:09.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:09.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:09.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:09.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:09.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:09.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:09.263][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-19 20:01:09.265][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:09.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-19 20:01:09.268][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:09.269][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:09.270][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:09.271][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:09.272][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:09.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:09.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:09.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:09.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:09.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:09.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:09.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:09.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:09.289][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-19 20:01:09.302][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:09.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:09.306][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-19 20:01:09.664][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-19 20:01:10.015][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:10.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-19 20:01:10.025][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-19 20:01:10.027][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-19 20:01:10.030][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:10.039][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:10.041][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:10.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:10.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:10.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:10.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:10.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:10.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:10.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:10.059][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.060][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.061][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.066][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:10.068][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:10.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.070][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:10.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.074][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:10.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:10.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.077][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:10.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:10.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:10.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:10.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.085][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:10.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:10.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.090][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.091][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.099][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:10.100][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:10.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.101][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.102][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:10.103][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.106][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:10.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.109][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:10.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:10.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.112][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:10.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:10.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.116][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:10.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:10.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.119][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:10.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:10.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.124][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:10.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:10.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.127][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.129][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:10.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:10.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.132][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:10.133][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:10.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.134][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:10.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:10.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:10.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:10.190][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-19 20:01:10.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:10.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:10.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:10.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:10.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:10.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:10.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:10.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:10.211][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[2024-11-19 20:01:10.212][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-19 20:01:10.224][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:10.225][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-19 20:01:10.226][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:10.227][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:10.228][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:10.229][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:10.230][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:10.231][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:10.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:10.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:10.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:10.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:10.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:10.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:10.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:10.244][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-19 20:01:10.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:10.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:10.249][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-19 20:01:10.581][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-19 20:01:10.916][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:10.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-19 20:01:10.921][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-19 20:01:10.924][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-19 20:01:10.926][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:10.928][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:10.929][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:10.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:10.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:10.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:10.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:10.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:10.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:10.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:10.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.957][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:10.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:10.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.962][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:10.963][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:10.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.965][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:10.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:10.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.970][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:10.971][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:10.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.972][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:10.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.978][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:10.979][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:10.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.980][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:10.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:10.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.986][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.987][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.988][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:10.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.994][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:10.995][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:10.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:10.997][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:10.998][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:10.999][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.001][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.002][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:11.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.006][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.007][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.009][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.015][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:11.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:11.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:11.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:11.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.023][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:11.024][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:11.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.026][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.028][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:11.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:11.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.032][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:11.033][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:11.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.034][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:11.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:11.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:11.086][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-19 20:01:11.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:11.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:11.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:11.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:11.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:11.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:11.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:11.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:11.111][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-19 20:01:11.112][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:11.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-19 20:01:11.116][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:11.117][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:11.118][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:11.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:11.119][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:11.120][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:11.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:11.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:11.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:11.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:11.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:11.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:11.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:11.134][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-19 20:01:11.137][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:11.138][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:11.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-19 20:01:11.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-19 20:01:11.808][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:11.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-19 20:01:11.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-19 20:01:11.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-19 20:01:11.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:11.822][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:11.823][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:11.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:11.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:11.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:11.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:11.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:11.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:11.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:11.838][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.841][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.846][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:11.847][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:11.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.848][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.850][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:11.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:11.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.862][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:11.863][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:11.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.864][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:11.870][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:11.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.871][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:11.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:11.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.876][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:11.877][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:11.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.889][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:11.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:11.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.894][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:11.895][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:11.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.897][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.898][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:11.899][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.901][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.902][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:11.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.906][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.907][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.913][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:11.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:11.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.916][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:11.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.921][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:11.922][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:11.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.924][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:11.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:11.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.928][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:11.929][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:11.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.931][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:11.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:11.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:11.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:11.982][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-19 20:01:11.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:11.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:11.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:11.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:11.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:11.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:11.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:12.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:12.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:12.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:12.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:12.007][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-19 20:01:12.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:12.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-19 20:01:12.010][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:12.011][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:12.013][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:12.014][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:12.015][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:12.016][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:12.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:12.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:12.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:12.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:12.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:12.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:12.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:12.032][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-19 20:01:12.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:12.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:12.039][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-19 20:01:12.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-19 20:01:12.773][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:12.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-19 20:01:12.779][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-19 20:01:12.783][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-19 20:01:12.785][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:12.786][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:12.788][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:12.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:12.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:12.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:12.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:12.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:12.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:12.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:12.801][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.803][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.805][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.810][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:12.811][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:12.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.812][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.813][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.818][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:12.819][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:12.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.820][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.827][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:12.828][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:12.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.829][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.844][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:12.845][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:12.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.847][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:12.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:12.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:12.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.854][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.855][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:12.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.858][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:12.864][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:12.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:12.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:12.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:12.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.875][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.880][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:12.881][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:12.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.885][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:12.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:12.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.889][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:12.890][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:12.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.891][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:12.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:12.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:12.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:12.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:12.936][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-19 20:01:12.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:12.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:12.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:12.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:12.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:12.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:12.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:12.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:12.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:12.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:12.965][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-19 20:01:12.966][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:12.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-19 20:01:12.968][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 20:01:12.969][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 20:01:12.971][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:12.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:12.972][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 20:01:12.973][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 20:01:12.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:12.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:12.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:12.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:12.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:12.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:12.985][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[2024-11-19 20:01:12.986][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-19 20:01:12.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 20:01:12.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 20:01:12.991][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-19 20:01:13.322][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-19 20:01:13.656][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 20:01:13.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-19 20:01:13.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-19 20:01:13.665][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-19 20:01:13.667][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 20:01:13.669][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:13.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:13.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:13.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:13.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:13.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:13.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:13.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:13.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:13.683][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.684][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.686][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.692][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:13.693][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:13.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.695][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:13.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:13.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.699][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:13.700][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:13.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:13.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:13.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:13.707][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:13.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.709][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:13.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:13.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.713][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.714][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:13.716][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:13.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.717][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.718][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:13.720][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.722][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.723][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.737][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.738][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.740][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.745][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:13.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:13.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.747][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:13.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:13.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:13.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:13.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.756][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:13.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.760][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:13.761][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:13.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.763][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:13.822][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-19 20:01:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:13.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:13.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:13.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:13.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:13.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:13.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:13.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:13.845][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-19 20:01:13.846][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:13.847][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-19 20:01:13.848][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:13.850][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-11-19 20:01:13.851][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:13.852][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:13.853][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:13.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:13.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:13.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:13.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:13.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:13.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:13.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:13.872][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.873][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.874][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.879][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:13.881][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:13.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.884][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.887][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:13.888][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:13.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.890][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:13.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.896][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:13.897][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:13.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.898][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.899][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:13.900][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:13.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.902][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.903][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:13.905][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:13.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.907][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.909][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:13.910][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.913][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.914][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:13.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.920][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:13.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.926][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:13.927][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.928][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:13.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:13.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.934][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:13.936][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:13.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.938][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.939][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:13.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:13.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:13.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.946][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:13.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:13.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:13.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:13.990][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-19 20:01:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:13.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:14.017][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-19 20:01:14.018][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:14.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-19 20:01:14.022][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:14.025][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-11-19 20:01:14.026][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:14.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:14.029][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:14.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:14.045][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.047][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.055][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.056][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.058][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.060][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.063][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.066][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.072][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.074][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.075][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.081][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.082][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.084][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.090][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.093][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.094][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.095][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.106][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.113][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.116][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.122][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.123][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.125][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.130][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.131][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.133][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.141][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.142][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.187][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-19 20:01:14.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:14.214][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-19 20:01:14.215][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:14.216][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-19 20:01:14.241][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:14.248][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2024-11-19 20:01:14.255][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:14.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:14.257][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:14.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:14.280][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.281][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.283][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.288][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.289][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.292][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.296][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.297][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.306][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.307][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.309][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.314][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.317][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.324][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.325][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.327][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.328][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.330][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.334][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.340][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.341][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.344][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.349][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.350][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.351][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.356][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.358][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.360][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.361][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.364][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.367][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.429][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-19 20:01:14.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:14.462][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-19 20:01:14.463][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:14.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-19 20:01:14.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:14.470][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2024-11-19 20:01:14.472][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:14.474][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:14.475][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:14.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:14.494][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.496][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.498][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.505][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.506][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.508][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.510][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.515][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.526][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.527][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.554][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.560][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.561][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.562][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.564][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.566][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.574][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.579][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.581][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.586][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.587][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.589][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.594][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.595][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.597][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.639][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-19 20:01:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:14.667][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-19 20:01:14.668][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:14.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-19 20:01:14.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:14.674][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2024-11-19 20:01:14.675][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:14.676][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:14.677][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:14.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:14.705][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.714][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.716][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.718][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.724][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.726][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.727][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.734][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.735][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.741][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.742][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.744][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.751][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.753][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.754][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.756][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.758][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.765][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.767][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.772][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.773][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.775][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.780][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.781][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.783][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.795][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.796][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.798][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.800][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:14.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.848][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-19 20:01:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:14.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.871][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[2024-11-19 20:01:14.872][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-19 20:01:14.873][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:14.875][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-19 20:01:14.876][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:14.878][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2024-11-19 20:01:14.880][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:14.881][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:14.883][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:14.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:14.886][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:14.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:14.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:14.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:14.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:14.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:14.901][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.904][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:14.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:14.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.909][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.910][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.912][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.918][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.923][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.924][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.925][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:14.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:14.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.930][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.933][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:14.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:14.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.938][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.939][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:14.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.947][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:14.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.950][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.953][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.959][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.960][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:14.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:14.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.964][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.967][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:14.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.973][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.975][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.981][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.982][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.984][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.990][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.991][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:14.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:14.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:14.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.046][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-19 20:01:15.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:15.073][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-19 20:01:15.074][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:15.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-19 20:01:15.077][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:15.079][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2024-11-19 20:01:15.080][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:15.082][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:15.083][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:15.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.099][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.100][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.108][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:15.109][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:15.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.111][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.113][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:15.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.117][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:15.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:15.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.119][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:15.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:15.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:15.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:15.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.129][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:15.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:15.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.136][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.137][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.139][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.154][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:15.155][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:15.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.157][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.159][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:15.160][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.161][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.166][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.167][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.169][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.180][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:15.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:15.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.183][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:15.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:15.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:15.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.190][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.191][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:15.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:15.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:15.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:15.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.199][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:15.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.247][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-19 20:01:15.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.271][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[2024-11-19 20:01:15.272][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-19 20:01:15.273][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:15.274][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-19 20:01:15.276][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:15.280][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-11-19 20:01:15.281][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:15.283][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:15.284][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:15.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.303][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.304][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.306][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.311][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:15.312][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:15.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.315][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:15.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:15.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.328][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:15.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:15.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.331][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:15.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:15.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.336][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:15.337][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:15.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.339][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:15.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:15.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.344][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.346][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:15.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.351][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:15.352][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:15.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.353][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.355][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:15.356][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.358][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:15.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.366][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.371][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:15.372][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:15.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.375][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:15.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:15.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.381][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:15.383][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:15.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.386][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:15.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:15.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.390][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:15.391][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:15.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.393][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.394][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:15.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:15.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:15.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.449][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-19 20:01:15.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.493][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[2024-11-19 20:01:15.496][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:15.498][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:15.499][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:15.501][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:01:15.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.715][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[2024-11-19 20:01:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.884][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.908][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[2024-11-19 20:01:15.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:15.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:15.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:15.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:15.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:15.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:15.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:15.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:15.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:15.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:15.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.020][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[2024-11-19 20:01:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.069][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[2024-11-19 20:01:16.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.159][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[2024-11-19 20:01:16.164][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:16.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-11-19 20:01:16.168][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:16.170][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-11-19 20:01:16.174][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[2024-11-19 20:01:16.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:16.180][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-11-19 20:01:16.182][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:16.184][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-11-19 20:01:16.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:16.201][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-19 20:01:16.202][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:16.204][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-19 20:01:16.205][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:16.207][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-11-19 20:01:16.208][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:16.210][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:16.211][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:16.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.226][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.228][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.234][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.240][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:16.241][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:16.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.243][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:16.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.248][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:16.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:16.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.251][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.256][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:16.257][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:16.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.259][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:16.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:16.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.267][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.272][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.273][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.276][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.281][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:16.282][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.289][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.290][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.292][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.298][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:16.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:16.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.301][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:16.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:16.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.307][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:16.307][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:16.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.309][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.311][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:16.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:16.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.316][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:16.317][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:16.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:16.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:16.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.381][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-19 20:01:16.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.441][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[2024-11-19 20:01:16.442][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-19 20:01:16.443][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:16.446][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-19 20:01:16.447][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:16.449][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-11-19 20:01:16.451][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:16.452][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:16.453][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:16.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.471][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.473][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.478][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:16.479][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:16.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.481][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:16.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:16.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.486][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:16.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:16.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:16.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:16.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.500][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:16.501][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:16.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.502][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:16.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:16.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.508][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.508][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.510][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:16.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.517][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:16.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.519][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.520][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:16.522][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.524][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.525][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.529][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.530][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.537][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:16.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:16.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.539][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:16.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:16.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.546][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:16.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:16.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.549][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:16.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:16.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.555][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:16.556][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:16.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.558][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.560][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:16.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:16.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:16.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:16.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.609][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-19 20:01:16.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.644][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[2024-11-19 20:01:16.647][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:16.649][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:16.650][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:16.652][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:01:16.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.667][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[2024-11-19 20:01:16.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.728][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.TRACE[2024-11-19 20:01:16.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.916][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.TRACE[2024-11-19 20:01:16.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.945][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.TRACE[2024-11-19 20:01:16.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:16.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:16.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:16.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:16.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:16.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:16.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:16.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:16.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.083][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.167][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.TRACE[2024-11-19 20:01:17.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.242][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.TRACE[2024-11-19 20:01:17.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.279][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[2024-11-19 20:01:17.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:17.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 20:01:17.287][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:17.289][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 20:01:17.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.486][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.TRACE[2024-11-19 20:01:17.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.749][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.TRACE[2024-11-19 20:01:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.807][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.TRACE[2024-11-19 20:01:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.916][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.TRACE[2024-11-19 20:01:17.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:17.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:17.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:17.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:17.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:17.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:17.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:17.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:17.990][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.TRACE[2024-11-19 20:01:17.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:17.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.024][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:18.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:18.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:18.041][biodb::testThat]
biodb.INFO [2024-11-19 20:01:18.042][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-19 20:01:18.043][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:18.045][biodb::testThat]
biodb.TRACE[2024-11-19 20:01:18.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 20:01:18.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 20:01:18.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:18.090][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[2024-11-19 20:01:18.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:18.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 20:01:18.097][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:18.099][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 20:01:18.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.134][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[2024-11-19 20:01:18.137][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:18.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 20:01:18.141][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:18.143][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 20:01:18.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.195][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:18.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.217][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.218][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.219][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.229][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.230][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.231][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.234][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.257][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 20:01:18.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.285][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.286][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.287][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.292][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.293][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.297][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.298][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.299][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.300][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.302][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.303][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.317][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:18.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.338][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.338][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.339][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.340][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.341][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.342][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.345][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.346][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.351][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.352][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.355][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.356][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.369][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 20:01:18.370][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:18.371][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:18.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:18.474][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[2024-11-19 20:01:18.478][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:18.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-19 20:01:18.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:18.484][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-19 20:01:18.487][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[2024-11-19 20:01:18.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:18.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-19 20:01:18.494][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:18.498][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-19 20:01:18.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.515][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[2024-11-19 20:01:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.618][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:18.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.668][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.668][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.669][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.670][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.671][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.674][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.675][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.678][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.679][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.680][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.683][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.684][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.697][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 20:01:18.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.745][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.746][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.747][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.747][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.748][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.749][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.750][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.752][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.753][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.756][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.765][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.767][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.768][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.769][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.770][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.786][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:18.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.797][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[2024-11-19 20:01:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.807][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.808][private$selectFields]
biodb.TRACE[2024-11-19 20:01:18.809][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:18.810][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:18.811][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.812][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.813][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.826][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.827][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.829][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.831][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.832][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:18.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.837][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.838][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:18.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.850][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 20:01:18.851][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:18.851][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:18.860][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:18.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:18.869][biodb::testThat]
biodb.INFO [2024-11-19 20:01:18.870][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-19 20:01:18.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:18.872][biodb::testThat]
biodb.TRACE[2024-11-19 20:01:18.876][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 20:01:18.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 20:01:18.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.916][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[2024-11-19 20:01:18.919][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[2024-11-19 20:01:18.922][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:18.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 20:01:18.925][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:18.927][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 20:01:18.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:18.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:18.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:18.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:18.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:18.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:18.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:18.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:18.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:18.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:18.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:18.958][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[2024-11-19 20:01:18.992][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:19.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 20:01:19.007][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:19.010][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 20:01:19.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.028][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[2024-11-19 20:01:19.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.078][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:19.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.089][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.TRACE[2024-11-19 20:01:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.100][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.101][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.102][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.104][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.110][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.113][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.114][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.115][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.118][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.119][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.141][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 20:01:19.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.160][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.160][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.161][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.162][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.165][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.169][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.170][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.171][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.172][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.174][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.175][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.188][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:19.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.199][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.TRACE[2024-11-19 20:01:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.209][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.210][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.210][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.211][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.212][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.215][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.216][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.217][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.219][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.220][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.221][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.231][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.243][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 20:01:19.254][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:19.255][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:19.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:19.296][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[2024-11-19 20:01:19.299][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:19.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-19 20:01:19.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:19.303][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-19 20:01:19.306][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[2024-11-19 20:01:19.309][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:19.311][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-19 20:01:19.312][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:19.316][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-19 20:01:19.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.390][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.TRACE[2024-11-19 20:01:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:19.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.413][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:19.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.426][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.TRACE[2024-11-19 20:01:19.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.448][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.448][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.449][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.450][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.451][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.453][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.454][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.457][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.458][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.460][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.465][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.466][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.489][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 20:01:19.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.518][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.519][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.520][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.522][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.525][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.528][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.529][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.530][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.533][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.534][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.536][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.537][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.538][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.540][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.541][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.557][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:19.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.568][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[2024-11-19 20:01:19.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.579][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.580][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.581][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.582][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.583][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.586][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.587][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.588][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.590][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.590][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.591][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.595][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.595][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 20:01:19.609][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:19.610][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:19.621][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:19.628][biodb::testThat]
biodb.INFO [2024-11-19 20:01:19.629][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-19 20:01:19.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:19.630][biodb::testThat]
biodb.TRACE[2024-11-19 20:01:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 20:01:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 20:01:19.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:19.679][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[2024-11-19 20:01:19.681][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:19.683][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 20:01:19.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:19.685][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 20:01:19.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.712][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[2024-11-19 20:01:19.716][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:19.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 20:01:19.718][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:19.720][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 20:01:19.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.735][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.TRACE[2024-11-19 20:01:19.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.780][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.TRACE[2024-11-19 20:01:19.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:19.793][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:19.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.812][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.813][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.814][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.815][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.817][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.818][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.819][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.821][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.822][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.823][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.825][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.826][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.827][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.830][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.831][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.848][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 20:01:19.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.870][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.871][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.872][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.873][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.878][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.880][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.882][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.884][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.885][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.888][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.889][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.910][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:19.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:19.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:19.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:19.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:19.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:19.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:19.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:19.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.935][private$selectFields]
biodb.TRACE[2024-11-19 20:01:19.937][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:19.938][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:19.939][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.943][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.944][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.945][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.947][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.950][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:19.951][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.952][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.955][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.956][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:19.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:19.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:19.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:19.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 20:01:19.973][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:19.974][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:20.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:20.046][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[2024-11-19 20:01:20.050][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:20.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-19 20:01:20.053][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:20.054][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-19 20:01:20.058][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[2024-11-19 20:01:20.062][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:20.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-19 20:01:20.064][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:20.066][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-19 20:01:20.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.092][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.138][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 20:01:20.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.160][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.160][private$selectFields]
biodb.TRACE[2024-11-19 20:01:20.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:20.163][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:20.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.177][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.178][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.230][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.238][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.240][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.241][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.242][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.243][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.245][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.247][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:20.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.285][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 20:01:20.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.311][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.312][private$selectFields]
biodb.TRACE[2024-11-19 20:01:20.313][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:20.314][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:20.315][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.320][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.321][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.323][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.324][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.326][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.328][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.330][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.331][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:20.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.344][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 20:01:20.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.356][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.TRACE[2024-11-19 20:01:20.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.367][private$selectFields]
biodb.TRACE[2024-11-19 20:01:20.368][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 20:01:20.369][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 20:01:20.370][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.371][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.372][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.373][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.375][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.376][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.377][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.378][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.379][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 20:01:20.381][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.382][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.385][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.386][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 20:01:20.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.405][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 20:01:20.406][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 20:01:20.407][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 20:01:20.439][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:20.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 20:01:20.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:20.447][biodb::testThat]
biodb.INFO [2024-11-19 20:01:20.448][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-19 20:01:20.450][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:20.451][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:20.452][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-19 20:01:20.453][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:20.455][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-19 20:01:20.457][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:20.459][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-11-19 20:01:20.460][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:20.461][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:20.462][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:20.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:20.478][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.481][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.487][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.488][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.490][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.491][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.492][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.493][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.494][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.495][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.497][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.498][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.500][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.502][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.504][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.505][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.507][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.509][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.513][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:20.514][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:20.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.516][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.517][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:20.518][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:20.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.525][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.526][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:20.527][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:20.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.529][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.579][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-19 20:01:20.580][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-19 20:01:20.601][biodb::testThat]
biodb.INFO [2024-11-19 20:01:20.603][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-19 20:01:20.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:20.606][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:20.628][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-19 20:01:20.629][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-19 20:01:20.630][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-19 20:01:20.632][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-19 20:01:20.636][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-11-19 20:01:20.642][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-11-19 20:01:20.643][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:20.644][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-19 20:01:20.645][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:20.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.656][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[2024-11-19 20:01:20.658][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.660][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.672][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.673][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.674][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.676][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.676][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.679][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.684][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.685][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.686][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.688][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.692][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.693][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.694][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.695][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.699][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.701][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:20.701][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:20.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.703][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.705][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:20.706][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:20.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.708][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:20.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:20.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.722][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.761][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[2024-11-19 20:01:20.763][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.764][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.766][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.772][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.773][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.776][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.777][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.782][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.783][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.786][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.792][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.793][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.795][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.800][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.801][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.802][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.808][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.812][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.814][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.818][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.819][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.821][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.823][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.836][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.837][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.839][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.844][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:20.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:20.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.848][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.854][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:20.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:20.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.857][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:20.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:20.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.864][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:20.865][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:20.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.867][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.869][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:20.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:20.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:20.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:20.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:20.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:20.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:20.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:20.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:20.916][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.TRACE[2024-11-19 20:01:20.919][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.922][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:20.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.933][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.934][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.936][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:20.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.944][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.946][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:20.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:20.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.952][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.955][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:20.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:20.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.959][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.963][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:20.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.968][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.969][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.972][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.973][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:20.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.977][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.978][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.980][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:20.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.987][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.988][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.990][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:20.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:20.996][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:20.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:20.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:20.999][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.004][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:21.005][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:21.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.007][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.008][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.012][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:21.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:21.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.014][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:21.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:21.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:21.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:21.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:21.082][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-19 20:01:21.083][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-19 20:01:21.084][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-19 20:01:21.100][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.101][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-19 20:01:21.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:21.103][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.153][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.155][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-19 20:01:21.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:21.157][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.168][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.169][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-19 20:01:21.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:21.172][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:21.175][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[2024-11-19 20:01:21.180][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:21.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-11-19 20:01:21.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:21.186][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-11-19 20:01:21.203][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:21.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:21.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.207][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:21.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:21.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:21.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:21.212][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 20:01:21.214][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.216][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-19 20:01:21.217][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:21.218][biodb::testThat]
biodb.ERROR[2024-11-19 20:01:21.236][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-19 20:01:21.266][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-19 20:01:21.286][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 20:01:21.287][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 20:01:21.289][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 20:01:21.290][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 20:01:21.291][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.294][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.296][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 20:01:21.317][biodb::testContext]
biodb.INFO [2024-11-19 20:01:21.318][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:21.319][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-19 20:01:21.321][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:21.322][biodb::testContext]
biodb.INFO [2024-11-19 20:01:21.325][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:21.327][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:21.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:21.334][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 20:01:21.335][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.340][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 20:01:21.342][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.345][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[2024-11-19 20:01:21.347][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 20:01:21.348][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.352][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 20:01:21.354][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 20:01:21.355][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 20:01:21.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.359][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[2024-11-19 20:01:21.360][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 20:01:21.361][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 20:01:21.363][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.367][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 20:01:21.368][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 20:01:21.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.373][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 20:01:21.374][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 20:01:21.376][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 20:01:21.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.379][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 20:01:21.381][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.386][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 20:01:21.387][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 20:01:21.388][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 20:01:21.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.393][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:21.394][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 20:01:21.395][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 20:01:21.397][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 20:01:21.398][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 20:01:21.399][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 20:01:21.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.402][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[2024-11-19 20:01:21.404][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 20:01:21.405][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 20:01:21.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.409][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 20:01:21.411][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 20:01:21.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.415][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 20:01:21.416][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 20:01:21.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.421][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 20:01:21.422][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 20:01:21.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.426][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[2024-11-19 20:01:21.427][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 20:01:21.429][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 20:01:21.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.433][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:21.435][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 20:01:21.463][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-19 20:01:21.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.467][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 20:01:21.469][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 20:01:21.470][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 20:01:21.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.474][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 20:01:21.477][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.478][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 20:01:21.479][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:21.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.483][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.485][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.487][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.488][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:21.489][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:21.491][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.492][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 20:01:21.492][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:21.493][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:21.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:21.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:21.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:21.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:21.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:21.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:21.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.504][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:21.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:21.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.509][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.510][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 20:01:21.512][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.514][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:21.515][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:21.518][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.519][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.520][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.521][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:21.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:21.523][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.524][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 20:01:21.525][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:21.526][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.527][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.528][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:21.528][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:21.528][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:21.528][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:21.528][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:21.529][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:21.530][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.533][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:21.534][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.535][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.536][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.537][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.538][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:21.539][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:21.540][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.541][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.542][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 20:01:21.543][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.544][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 20:01:21.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:21.547][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.548][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.549][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.550][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.551][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:21.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:21.553][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.554][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 20:01:21.555][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:21.556][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.557][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.558][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.559][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:21.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.562][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:21.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.565][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.566][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:21.568][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:21.569][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.570][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.571][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 20:01:21.573][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.574][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:21.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.576][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:21.576][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.579][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.580][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.581][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:21.582][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:21.583][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.584][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 20:01:21.585][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:21.586][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.588][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.588][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.589][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:21.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:21.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.596][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.597][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:21.598][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:21.598][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.599][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:21.600][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:21.601][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.685][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 20:01:21.686][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 20:01:21.688][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 20:01:21.689][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 20:01:21.691][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:21.692][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 20:01:21.693][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:21.694][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:21.696][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 20:01:21.697][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 20:01:21.698][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:21.700][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 20:01:21.701][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:21.703][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:21.704][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 20:01:21.705][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 20:01:21.707][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 20:01:21.708][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 20:01:21.709][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:21.711][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 20:01:21.713][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 20:01:21.714][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 20:01:21.716][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 20:01:21.717][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 20:01:21.718][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 20:01:21.720][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 20:01:21.721][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 20:01:21.723][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 20:01:21.724][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 20:01:21.725][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 20:01:21.727][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 20:01:21.728][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 20:01:21.729][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 20:01:21.731][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 20:01:21.732][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 20:01:21.733][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 20:01:21.734][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 20:01:21.736][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 20:01:21.737][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 20:01:21.738][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 20:01:21.739][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 20:01:21.741][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 20:01:21.743][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 20:01:21.744][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 20:01:21.746][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 20:01:21.747][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 20:01:21.749][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 20:01:21.750][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 20:01:21.752][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 20:01:21.753][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 20:01:21.755][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 20:01:21.756][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 20:01:21.757][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 20:01:21.759][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 20:01:21.760][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 20:01:21.762][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 20:01:21.763][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 20:01:21.764][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 20:01:21.766][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 20:01:21.767][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 20:01:21.769][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 20:01:21.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 20:01:21.772][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 20:01:21.773][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 20:01:21.774][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 20:01:21.775][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 20:01:21.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:21.778][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:21.780][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 20:01:21.781][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 20:01:21.782][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 20:01:21.784][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 20:01:21.785][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 20:01:21.787][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 20:01:21.788][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 20:01:21.789][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 20:01:21.791][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 20:01:21.792][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 20:01:21.794][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 20:01:21.795][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 20:01:21.796][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 20:01:21.798][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 20:01:21.799][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 20:01:21.800][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 20:01:21.802][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:21.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:21.804][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.807][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[2024-11-19 20:01:21.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.814][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[2024-11-19 20:01:21.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.847][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[2024-11-19 20:01:21.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.871][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[2024-11-19 20:01:21.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.901][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[2024-11-19 20:01:21.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.916][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[2024-11-19 20:01:21.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:21.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:21.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:21.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:21.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:21.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:21.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:21.934][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:21.936][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 20:01:21.938][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.939][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.942][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:21.943][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.945][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.946][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 20:01:21.947][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 20:01:21.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:21.949][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.951][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 20:01:21.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 20:01:21.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 20:01:21.954][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:21.955][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:21.955][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:21.955][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:21.956][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 20:01:21.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:21.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:21.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:21.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:21.963][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:21.963][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 20:01:21.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:21.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:21.966][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:21.967][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 20:01:21.967][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 20:01:21.969][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:21.971][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:21.973][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 20:01:21.975][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:21.976][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:21.978][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:21.981][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 20:01:21.982][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 20:01:21.984][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 20:01:21.985][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 20:01:21.986][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:21.987][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:21.989][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 20:01:21.990][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 20:01:21.992][biodb::testThat]
biodb.INFO [2024-11-19 20:01:21.993][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-19 20:01:21.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:21.994][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:21.999][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 20:01:22.003][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 20:01:22.006][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.009][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 20:01:22.013][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[2024-11-19 20:01:22.016][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-19 20:01:22.019][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.021][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-19 20:01:22.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.035][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[2024-11-19 20:01:22.039][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.047][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-19 20:01:22.048][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.051][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-19 20:01:22.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.101][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[2024-11-19 20:01:22.105][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-19 20:01:22.108][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.110][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-19 20:01:22.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.127][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[2024-11-19 20:01:22.131][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-19 20:01:22.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.136][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-19 20:01:22.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.151][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.DEBUG[2024-11-19 20:01:22.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.170][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[2024-11-19 20:01:22.174][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.176][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-19 20:01:22.178][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.179][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-19 20:01:22.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.197][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[2024-11-19 20:01:22.201][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.202][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-19 20:01:22.204][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.205][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-19 20:01:22.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.223][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[2024-11-19 20:01:22.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-11-19 20:01:22.230][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.233][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-11-19 20:01:22.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.246][FUN] Functions in observer BiodbConfig: [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 [2024-11-19 20:01:22.254][biodb::testThat]
biodb.INFO [2024-11-19 20:01:22.255][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-19 20:01:22.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:22.257][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:22.261][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[2024-11-19 20:01:22.266][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.267][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-11-19 20:01:22.269][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.270][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-11-19 20:01:22.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.289][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[2024-11-19 20:01:22.292][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.294][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-11-19 20:01:22.295][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.297][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-11-19 20:01:22.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:22.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.309][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 [2024-11-19 20:01:22.316][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 20:01:22.317][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 20:01:22.319][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 20:01:22.319][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 20:01:22.320][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.322][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.324][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.324][FUN] Functions in observer BiodbConfig: [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 [2024-11-19 20:01:22.328][biodb::testContext]
biodb.INFO [2024-11-19 20:01:22.329][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:22.330][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-19 20:01:22.331][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:22.332][biodb::testContext]
biodb.INFO [2024-11-19 20:01:22.336][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:22.339][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:22.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:22.351][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 20:01:22.352][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.356][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 20:01:22.357][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.361][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 20:01:22.362][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.366][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 20:01:22.367][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 20:01:22.368][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 20:01:22.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.372][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 20:01:22.373][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 20:01:22.374][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.378][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 20:01:22.379][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 20:01:22.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.382][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[2024-11-19 20:01:22.383][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 20:01:22.384][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 20:01:22.385][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 20:01:22.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.388][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 20:01:22.389][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.392][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 20:01:22.393][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 20:01:22.394][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 20:01:22.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.398][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:22.398][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 20:01:22.399][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 20:01:22.400][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 20:01:22.401][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 20:01:22.402][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 20:01:22.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.405][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 20:01:22.406][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 20:01:22.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.409][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 20:01:22.410][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 20:01:22.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.413][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[2024-11-19 20:01:22.413][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 20:01:22.414][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 20:01:22.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.417][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 20:01:22.418][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 20:01:22.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.421][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.DEBUG[2024-11-19 20:01:22.422][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 20:01:22.422][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 20:01:22.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.425][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:22.426][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 20:01:22.466][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-19 20:01:22.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.471][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 20:01:22.472][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 20:01:22.473][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 20:01:22.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.477][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 20:01:22.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.480][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 20:01:22.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:22.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.485][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.486][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.487][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:22.488][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:22.489][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.490][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 20:01:22.491][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:22.492][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:22.494][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:22.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:22.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.505][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:22.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.508][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.509][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:22.511][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:22.512][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.512][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.513][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 20:01:22.515][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.517][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:22.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:22.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:22.524][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:22.525][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.526][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 20:01:22.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:22.529][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.530][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.531][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:22.531][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:22.531][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:22.531][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:22.531][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:22.532][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:22.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.535][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:22.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.537][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.539][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.540][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:22.541][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:22.542][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.543][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.544][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 20:01:22.546][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.547][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 20:01:22.548][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:22.551][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.552][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.553][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.554][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.555][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:22.556][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:22.557][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.558][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 20:01:22.559][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:22.560][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.562][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:22.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.566][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:22.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.570][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:22.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:22.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.574][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.575][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 20:01:22.577][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.578][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:22.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.581][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:22.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.582][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.586][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:22.587][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:22.587][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.588][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 20:01:22.589][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:22.590][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.592][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.594][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:22.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:22.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.600][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.601][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.602][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:22.603][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:22.604][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.605][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:22.606][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:22.607][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.607][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[2024-11-19 20:01:22.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.626][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[2024-11-19 20:01:22.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.685][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 20:01:22.687][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 20:01:22.688][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 20:01:22.690][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 20:01:22.692][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:22.693][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 20:01:22.694][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:22.696][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:22.698][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 20:01:22.699][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 20:01:22.701][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:22.702][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 20:01:22.703][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:22.705][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:22.707][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 20:01:22.708][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 20:01:22.709][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 20:01:22.711][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 20:01:22.712][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:22.714][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 20:01:22.715][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 20:01:22.717][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 20:01:22.719][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 20:01:22.720][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 20:01:22.722][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 20:01:22.723][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 20:01:22.724][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 20:01:22.726][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 20:01:22.728][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 20:01:22.729][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 20:01:22.731][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 20:01:22.732][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 20:01:22.734][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 20:01:22.735][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 20:01:22.737][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 20:01:22.739][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 20:01:22.741][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 20:01:22.742][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 20:01:22.744][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 20:01:22.745][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 20:01:22.747][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 20:01:22.748][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 20:01:22.750][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 20:01:22.751][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 20:01:22.752][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 20:01:22.754][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 20:01:22.755][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 20:01:22.757][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 20:01:22.758][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 20:01:22.760][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 20:01:22.761][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 20:01:22.763][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 20:01:22.764][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 20:01:22.766][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 20:01:22.767][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 20:01:22.768][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 20:01:22.770][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 20:01:22.772][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 20:01:22.773][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 20:01:22.775][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 20:01:22.776][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 20:01:22.778][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 20:01:22.779][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 20:01:22.780][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 20:01:22.782][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 20:01:22.783][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 20:01:22.785][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:22.786][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:22.788][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 20:01:22.789][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 20:01:22.790][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 20:01:22.792][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 20:01:22.793][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 20:01:22.795][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 20:01:22.796][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 20:01:22.797][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 20:01:22.798][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 20:01:22.800][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 20:01:22.801][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 20:01:22.802][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 20:01:22.804][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 20:01:22.806][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 20:01:22.807][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 20:01:22.808][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 20:01:22.810][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:22.811][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:22.812][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.814][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.854][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[2024-11-19 20:01:22.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.884][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[2024-11-19 20:01:22.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.902][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[2024-11-19 20:01:22.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.908][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[2024-11-19 20:01:22.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:22.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:22.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:22.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:22.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:22.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:22.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:22.922][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:22.924][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 20:01:22.925][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.926][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:22.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.932][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.933][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 20:01:22.934][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 20:01:22.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:22.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.936][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 20:01:22.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 20:01:22.939][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 20:01:22.940][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:22.941][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:22.941][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:22.941][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:22.942][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 20:01:22.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.945][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:22.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:22.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:22.947][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:22.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:22.948][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 20:01:22.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:22.950][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:22.951][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:22.952][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 20:01:22.952][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 20:01:22.953][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:22.954][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:22.956][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 20:01:22.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:22.958][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:22.960][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:22.963][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 20:01:22.964][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 20:01:22.965][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 20:01:22.966][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 20:01:22.967][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:22.968][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:22.969][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 20:01:22.970][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 20:01:22.971][biodb::testThat]
biodb.INFO [2024-11-19 20:01:22.972][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-19 20:01:22.973][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:22.974][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:22.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 20:01:22.980][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.981][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 20:01:22.982][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.984][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 20:01:22.988][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[2024-11-19 20:01:22.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:22.992][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-19 20:01:22.993][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:22.998][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-11-19 20:01:23.008][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 20:01:23.009][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 20:01:23.010][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 20:01:23.011][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 20:01:23.012][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.013][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.015][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 20:01:23.022][biodb::testContext]
biodb.INFO [2024-11-19 20:01:23.024][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:23.025][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-19 20:01:23.026][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 20:01:23.027][biodb::testContext]
biodb.INFO [2024-11-19 20:01:23.029][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:23.031][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:23.036][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:23.037][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 20:01:23.038][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.042][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 20:01:23.043][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.047][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 20:01:23.048][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.052][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 20:01:23.053][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 20:01:23.054][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 20:01:23.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.058][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 20:01:23.059][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 20:01:23.060][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.064][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 20:01:23.065][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 20:01:23.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.068][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 20:01:23.070][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 20:01:23.071][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 20:01:23.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.074][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 20:01:23.075][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.079][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 20:01:23.080][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 20:01:23.081][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 20:01:23.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.085][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:23.086][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 20:01:23.087][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 20:01:23.088][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 20:01:23.089][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 20:01:23.090][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 20:01:23.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.094][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 20:01:23.095][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 20:01:23.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.099][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 20:01:23.101][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 20:01:23.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.103][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[2024-11-19 20:01:23.104][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 20:01:23.105][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 20:01:23.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.108][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 20:01:23.109][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 20:01:23.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.112][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 20:01:23.113][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 20:01:23.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.117][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 20:01:23.119][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 20:01:23.143][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-19 20:01:23.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.147][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 20:01:23.149][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 20:01:23.150][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 20:01:23.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.154][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 20:01:23.155][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.156][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 20:01:23.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.158][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:23.159][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.161][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.162][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.163][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:23.164][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:23.165][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.166][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 20:01:23.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:23.168][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.169][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:23.171][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:23.171][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:23.171][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:23.171][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:23.172][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:23.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.175][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:23.176][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.178][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.179][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.180][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:23.181][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:23.182][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.183][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.184][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 20:01:23.186][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.187][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:23.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.189][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:23.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.194][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:23.195][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:23.196][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.197][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 20:01:23.199][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:23.200][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.207][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:23.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:23.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:23.208][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 20:01:23.208][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 20:01:23.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:23.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.213][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:23.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.217][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:23.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:23.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.221][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.222][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 20:01:23.223][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.225][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 20:01:23.226][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.227][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:23.228][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.229][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.231][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.233][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 20:01:23.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:23.235][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.236][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 20:01:23.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:23.238][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.239][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.240][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:23.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.244][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:23.245][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.246][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.246][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.248][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.249][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:23.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:23.251][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.252][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.253][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 20:01:23.255][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.256][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 20:01:23.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:23.259][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.260][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.261][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.263][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 20:01:23.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:23.265][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.266][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 20:01:23.267][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:23.268][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.269][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.270][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.271][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 20:01:23.273][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.274][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.275][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:23.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.278][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.279][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:23.281][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:23.282][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.284][self$setPropertyValue]
biodb.DEBUG[2024-11-19 20:01:23.285][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:23.286][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.287][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[2024-11-19 20:01:23.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.303][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[2024-11-19 20:01:23.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.340][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[2024-11-19 20:01:23.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.352][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[2024-11-19 20:01:23.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.356][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[2024-11-19 20:01:23.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.362][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 20:01:23.364][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 20:01:23.365][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 20:01:23.367][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 20:01:23.368][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:23.369][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 20:01:23.371][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:23.372][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:23.374][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 20:01:23.375][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 20:01:23.376][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:23.378][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 20:01:23.379][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 20:01:23.380][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 20:01:23.382][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 20:01:23.383][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 20:01:23.384][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 20:01:23.386][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 20:01:23.387][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:23.389][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 20:01:23.391][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 20:01:23.392][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 20:01:23.394][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 20:01:23.395][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 20:01:23.397][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 20:01:23.398][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 20:01:23.400][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 20:01:23.401][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 20:01:23.402][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 20:01:23.404][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 20:01:23.405][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 20:01:23.407][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 20:01:23.408][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 20:01:23.410][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 20:01:23.411][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 20:01:23.412][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 20:01:23.414][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 20:01:23.415][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 20:01:23.417][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 20:01:23.418][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 20:01:23.419][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 20:01:23.421][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 20:01:23.422][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 20:01:23.424][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 20:01:23.425][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 20:01:23.426][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 20:01:23.427][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 20:01:23.429][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 20:01:23.430][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 20:01:23.432][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 20:01:23.433][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 20:01:23.434][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 20:01:23.436][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 20:01:23.438][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 20:01:23.439][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 20:01:23.441][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 20:01:23.442][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 20:01:23.443][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 20:01:23.445][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 20:01:23.446][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 20:01:23.447][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 20:01:23.449][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 20:01:23.450][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 20:01:23.451][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 20:01:23.453][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 20:01:23.454][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 20:01:23.455][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:23.456][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:23.458][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 20:01:23.459][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 20:01:23.460][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 20:01:23.461][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 20:01:23.463][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 20:01:23.464][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 20:01:23.465][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 20:01:23.466][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 20:01:23.468][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 20:01:23.470][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 20:01:23.471][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 20:01:23.472][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 20:01:23.473][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 20:01:23.475][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 20:01:23.476][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 20:01:23.477][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 20:01:23.479][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 20:01:23.480][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 20:01:23.481][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.482][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.483][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[2024-11-19 20:01:23.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.495][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[2024-11-19 20:01:23.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.501][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[2024-11-19 20:01:23.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.543][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[2024-11-19 20:01:23.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.548][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[2024-11-19 20:01:23.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.561][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[2024-11-19 20:01:23.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.583][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[2024-11-19 20:01:23.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 20:01:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 20:01:23.591][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 20:01:23.592][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 20:01:23.594][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.595][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.596][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.597][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 20:01:23.598][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.599][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.600][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.601][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 20:01:23.602][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 20:01:23.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 20:01:23.604][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.605][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 20:01:23.606][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 20:01:23.607][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 20:01:23.608][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 20:01:23.609][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 20:01:23.609][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 20:01:23.609][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 20:01:23.610][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 20:01:23.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.613][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 20:01:23.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 20:01:23.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 20:01:23.615][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 20:01:23.616][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 20:01:23.616][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 20:01:23.617][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 20:01:23.618][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 20:01:23.618][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 20:01:23.619][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 20:01:23.619][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 20:01:23.621][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 20:01:23.622][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 20:01:23.624][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 20:01:23.625][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 20:01:23.627][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 20:01:23.629][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 20:01:23.632][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 20:01:23.633][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 20:01:23.634][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 20:01:23.636][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 20:01:23.637][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:23.638][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 20:01:23.639][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 20:01:23.640][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 20:01:23.641][biodb::testThat]
biodb.INFO [2024-11-19 20:01:23.642][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-19 20:01:23.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 20:01:23.644][biodb::testThat]
biodb.DEBUG[2024-11-19 20:01:23.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 20:01:23.651][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:23.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 20:01:23.653][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:23.654][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 20:01:23.658][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[2024-11-19 20:01:23.661][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 20:01:23.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-19 20:01:23.664][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:23.665][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-19 20:01:23.670][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-19 20:01:23.671][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 20:01:23.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-19 20:01:23.674][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 20:01:23.677][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-11-19 20:01:23.678][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 20:01:23.680][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 20:01:23.681][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 20:01:23.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 20:01:23.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 20:01:23.697][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.698][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.701][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.707][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:23.708][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:23.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.710][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.711][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 20:01:23.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 20:01:23.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.715][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:23.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:23.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.718][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 20:01:23.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 20:01:23.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.723][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 20:01:23.724][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 20:01:23.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.727][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 20:01:23.728][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 20:01:23.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.731][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.732][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:23.734][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:23.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.736][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.737][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:23.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 20:01:23.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.741][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:23.742][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:23.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.744][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.746][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 20:01:23.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 20:01:23.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:23.751][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:23.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.753][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:23.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 20:01:23.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.759][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:23.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:23.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.762][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 20:01:23.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 20:01:23.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.768][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:23.768][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:23.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.770][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.772][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 20:01:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 20:01:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.775][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:23.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:23.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.779][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 20:01:23.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 20:01:23.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 20:01:23.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 20:01:23.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 20:01:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 20:01:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 20:01:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 20:01:23.825][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-19 20:01:23.829][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 20:01:23.830][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 20:01:23.831][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 20:01:23.832][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 20:01:23.833][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 20:01:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 20:01:23.835][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 20:01:23.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 20:01:23.837][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 20:01:23.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 371 ]
>
> proc.time()
user system elapsed
17.170 1.341 31.891
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 2.845 | 1.930 | 16.244 | |
| ChebiEntry | 0.355 | 0.034 | 0.753 | |